Syracuse University Partners With Serum Institute Of India To Develop Vaccines For Children

Amidst all the high explosives and illicit drugs comes a positive site addition about two very nasty toxins.  Several science news services (Eureka Alert, bio-medicine.org, and firstscience.com to start) posted the following article from Judy Holmes, the Dean of Arts and Sciences Senior Publications Coordinator, about a new project being started up to develop new oral vaccines for both tetanus and rotavirus.  Details below.

Chemistry assistant professor Robert Doyle will lead the research project.

A unique partnership between Syracuse University and the Serum Institute of India could lead to better access to life-saving vaccines for children living in some of the most impoverished areas of the world. The Institute recently awarded $250,000 to a team of SU researchers led by Robert Doyle, assistant professor of chemistry in the College of Arts and Sciences, to develop new oral vaccines against tetanus and rotavirus, a severe form of diarrhea that affects infants and young children worldwide.

Tetanus is caused by a toxin produced by bacteria naturally found in soil. The vaccine is only available by injection. While the disease is rare in the Western world, tetanus caused an estimated 257,000 deaths in low-income countries between 2000 and 2003, according to the World Health Organization‘s (WHO) latest report. A significant percentage involved infants born in predominately rural areas who were exposed to the tetanus bacteria during unsanitary delivery procedures. Likewise, infants and young children in these same countries have a much higher risk of dying from rotavirus than those living in Western nations. The disease killed an estimated 500,000 children in developing nations during 2004, according to a 2007 WHO report.

“We are very excited to be working with the Serum Institute of India on these projects,” Doyle says. “This is a difficult area of research due to the nature of the molecules we will be working with. But, if we are successful, our work could have an enormously positive impact on the lives of people well beyond Syracuse University. This is truly scholarship in action.”

Founded in 1966, the Serum Institute of India produces and supplies low-cost, life-saving vaccines for children and adults living in low-income countries. It is the world’s largest producer of measles and diphtheria-tetanus-pertussis (DPT) vaccines. An estimated two out of every three immunized children in the world have received a vaccine manufactured by the Serum Institute.

“Our company’s philanthropic philosophy is to make high-quality, affordable, life-saving vaccines available for under-privileged children in both India and in more than 140 countries across the world,” says S.V.Kapre, executive director of the Serum Institute of India. “This new partnership with Syracuse University will help the Serum Institute further this endeavor as it will open new doors of vaccine usage.”

The Institute approached Doyle because of his successful research to develop an oral form of insulin, which may someday enable people with insulin-dependent diabetes to take fewer daily injections. An oral vaccine for tetanus would enhance distribution in impoverished countries. Doyle’s team will also explore new ways to synthesize the rotavirus vaccine to make it more accessible to children in developing nations.

A new laboratory has been established in SU’s Center for Science and Technology for the research, which poses a number of challenges. Similarly to insulin, the protein molecules used in the tetanus vaccine are destroyed in the digestive system. However, the tetanus molecules are 30 times larger than insulin, making them more difficult to transport. The vaccine is created by literally boiling the tetanus bacteria in a chemical solution, causing the protein to completely unfold. In its new, unfolded state, the tetanus protein is harmless, but is still recognized as tetanus by the immune system so as to trigger a response that protects the person from the disease.

“It’s like frying an egg,” Doyle says. “The egg white, which is a protein, is clear when you crack the egg into a pan. When the egg heats up, the egg white becomes opaque as the protein unfolds. You still recognize it as an egg, but you can’t make the egg white clear again after it’s been heated.”

The challenge is to figure out how to package this large molecule, sneak it through the digestive system unharmed, and transport it through the wall of the small intestine where it can be absorbed into the bloodstream. “Tetanus is a strange and wonderful molecule,” Doyle says. “We need to get a better idea of what the unfolded protein looks like and try to predict areas that would make good targets for attaching a transport vehicle.”

Problem is, you can’t actually see a protein molecule or the thousands of chemical reactions that take place within it over nanoseconds of time. However, researchers can develop computerized models of the molecules to predict their behavior and zoom in on possible targets. Damian Allis, research professor in the chemistry department, will be developing models for both projects. “The simulations allow us to view the process and identify sticky ends of the proteins that could potentially be used as binding sites for transport molecules,” Allis says.

Unlike the tetanus vaccine molecule, the rotavirus molecule Doyle’s team will be working with is not a protein; it is a viral capsule—the outer core of which is coated with proteins. “It’s a totally different problem,” Doyle says. “We need to deliver the viral capsid to the wall of the small intestine and keep it there long enough to trigger an immune response directly in the intestine, which is the first line of defense against the disease.”

Current oral rotavirus vaccines use tiny amounts of weakened, live bacteria. The vaccines’ possible side effects limit distribution in countries where access to health care is not readily available, according to the World Health Organization. Doyle’s aim is to develop a vaccine that does not contain live bacteria and has fewer side effects. The results could lead to wider distribution in low-income countries, ultimately saving hundreds of thousands of lives.

“We have some strong ideas and some good people on our team who bring very different skill sets to these projects,” Doyle says. “The University has been very supportive of this research. Every penny of the grant will go into research. It’s now up to us; we are excited about the possibilities.”

… and a pruned flavor of the same article with hard numbers from genengnews.com below.

Syracuse University (SU) and the Serum Institute of India will partner to develop new oral vaccines against tetanus and rotavirus. The institute awarded $250,000 to SU.

The aim of the rotavirus research is to develop a vaccine that does not contain live bacteria and has fewer side effects. Research will also explore new ways to synthesize the rotavirus vaccine to make it more accessible to children in developing nations, according to the companies.

The challenge with the tetanus protein is to figure out how to package this large molecule, get it through the digestive system unharmed, and transport it through the wall of the small intestine where it can be absorbed into the bloodstream. The SU team will develop computerized models to predict the behavior of these molecules

“The simulations allow us to view the process and identify sticky ends of the proteins that could potentially be used as binding sites for transport molecules,â€? explains Damian Allis, research professor in the chemistry department who will create these models.

For more information about the articles, contact Judy Holmes (jlholmes@syr.edu, 315-443-8085).  For more about the project, myself or Rob Doyle.

www.somewhereville.com/?p=123
www.somewhereville.com/?p=126
www.eurekalert.org
www.bio-medicine.org
www.firstscience.com
www.eurekalert.org/pub_releases/2008-09/su-sup090408.php
www.bio-medicine.org/biology-news-1/Syracuse-University-partners-with-Serum-Institute-of-India…
www.firstscience.com/home/news/biology/syracuse-university-partners-with-serum-institute-of-india…
thecollege.syr.edu/pressrelease/seruminstitute.htm
thecollege.syr.edu
en.wikipedia.org/wiki/Tetanus
en.wikipedia.org/wiki/Rotavirus
chemistry.syr.edu/faculty/doyle.html
www.syr.edu
www.seruminstitute.com
en.wikipedia.org/wiki/Vaccine
www.who.int/en
www.somewhereville.com/?p=103
www.genengnews.com
www.genengnews.com/news/bnitem.aspx?name=41348596
chemistry.syr.edu/faculty/doyle_group/index.html

Changes To ions.itp Format For AMBER Implementations In GROMACS 3.3.x

No idea how to best propagate a change in a text file (amber_ions.txt) needed for running a force field (ffAMBER) in an open source program (GROMACS), so letting the RSS aggregators do as much of the work as possible.

Alan Wilter S. da Silva, D.Sc., CCPN Research Associate,Department of Biochemistry, University of Cambridge (yes, that one), pointed out a formatting error in the previous version of my ions.itp file (posted on this site as amber_ions.itp, which only identifies it as an AMBER-specific file).

My previous version looked like the following:

#ifdef _FF_AMBER94

[ moleculetype ]
; molname       nrexcl
Cl              1
[ atoms ]

; id    at type         res nr  residu name     at name  cg     nr        mass
1       amber94_30      1       Cl              Cl       -1     1         35.45000
#endif

#ifdef _FF_AMBER99

[ moleculetype ]
; molname       nrexcl
Cl              1
[ atoms ]

; id    at type         res nr  residu name     at name  cg     nr        mass
1       amber99_30      1       Cl              Cl       -1     1         35.4500
#endif

What I had done, and this was obvious once I looked at it (always after), was wrongly separated cgnr into cg and nr, neglected the label of the charge column and, therefore, took cg to be charge. These last two numbers were all correct by their value, but wrong in their order. The new format is as follows:

#ifdef _FF_AMBER94

[ moleculetype ]
; molname       nrexcl
Cl              1
[ atoms ]

; id    at type         res nr  residu name     at name  cgnr   charge    mass
1       amber94_30      1       Cl              Cl       1      -1        35.45000
#endif

#ifdef _FF_AMBER99

[ moleculetype ]
; molname       nrexcl
Cl              1
[ atoms ]

; id    at type         res nr  residu name     at name  cgnr   charge    mass
1       amber99_30      1       Cl              Cl       1      -1        35.4500
#endif

Changes have been made to the amber_ions.itp file on the original blog post and is available for download at: amber_ions.txt (download, change .txt to .itp, change amber_ions.itp to ions.itp, place into your ../top folder. This ions.itp file contains the GROMOS charges as well, just additional text for AMBER, so you can write right over the original). I hope no one out there has lost any sleep over their positive chloride ions.

chemistry.csulb.edu/ffamber
www.gromacs.org
www.bio.cam.ac.uk/~awd28
www.bio.cam.ac.uk
www.cam.ac.uk
www.somewhereville.com/?p=114

sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1

NOTE: This script works with additions to the ffG53a5/6.rtp (residue topology) files. This information is available at Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1.

The script below is the precursor to the ffAMBER/NAMOT/GROMACS script posted previously. This script takes the output of a NAMOT or NAMOT2 DNA structure generation (.pdb) and does all of the atom label and atom label position conversions, correct 3′and 5′terminal H atom assignments, and makes changes throughout the .pdb file to provide something that should flow seamlessly into the GROMACS pdb2gmx .top generator for the GROMOS96 force field.

To reiterate a previous point: Did you need to post the entire script and not just provide the downloadable text file as a link? Of course, as I suspect no small number of people looking for how to convert a NAMOT pdb file into GROMOS96-speak will begin by searching based on GROMACS errors, which occur one missing residue label at a time. Hopefully, having the entire script readable by google and yahoo will cause it to pop up high in the search ranking.

The problem in the ffAMBER script with thymine (the lack of methyl hydrogens in the NAMOT and NAMOT2 pdb output) isn’t a problem for GROMOS96, as these hydrogen atoms (and all non-polar (C-H) hydrogen atoms) are subsumed into their associated carbons. That is, only DNA O-H, N-H, and pi-system C-H hydrogens are considered in the GROMOS96 force field.

How to use:

As a series of sed operations, you obviously need sed, which is available for all platforms and “pre-installed” with any self-respecting Linux/UNIX distro (which, of course, means OSX (the OS under which the script was generated).

To run this script, have the script and your NAMOT/NAMOT2-generated .pdb in the same directory and type:

./NAMOT_to_GROMOS96_in_GROMACS.script FILENAME.pdb NN

Where:

NAMOT_to_GROMOS96_in_GROMACS.script is the name of the script

FILENAME.pdb is the .pdb file (include the .pdb)

NN is the number of bases in each strand. This number is required in order to correctly change the atom types on the 3′ end of each strand.

This script is downloadable form the following link: NAMOT_to_GROMOS96_in_GROMACS.script

I also include a 35-base C-G double helix NAMOT .pdb file at C_G_NAMOT.pdb. To test the script on your machine, type the following in a Terminal window:

./NAMOT_to_GROMOS96_in_GROMACS.script C_G_NAMOT.pdb 35

As usual, if you have problems, comments, questions, concerns, etc. please either make an account and post a comment for this post or send me an email and I’ll keep the running tally.

##############################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
# This script takes the double helix output from NAMOT and NAMOT2 (a and b
# strands) and converts them into a format that the current GROMOS96 (53a6/5)
# force field in GROMACS can use in the generation of the GROMACS .top file.
#
################################################################################
#
# Generally, the following list of GROMACS runs should get you through an
# energy minimization without problem.  Note only 10 cations are added
# to your structure.  Change accordingly (or don't.  It doesn't matter for
# the test).
#
# Run these in order:
#
# pdb2gmx -nomerge -f DNA.pdb -o DNA_pdb2gmx.gro -p DNA_pdb2gmx.top
# editconf -f DNA_pdb2gmx.gro -o DNA_editconf.gro -d 1.0 -bt triclinic
# genbox -cp DNA_editconf.gro -cs -o DNA_genbox.gro -p DNA_pdb2gmx.top
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr
# genion -np 10 -norandom -pname Na -o DNA_genion.gro -s DNA_gromppem.tpr
#   -p DNA_pdb2gmx.top (this .top goes in the same line as the genion)
# grompp -f em -c DNA_genion.gro -p DNA_pdb2gmx.top -o DNA_grompp2em.tpr2
# mdrun -s DNA_grompp2em.tpr -o DNA_md_em.trr -c DNA_md_em.pdb -v
#
################################################################################
#
# In case you don't have one handy, here's the contents of an em.mpd file
# for use in the energy minimization test.
#
# Copy this content below, remove the "#", save as a text filed named
# -> em.mpd
#
# cpp                 =  /usr/bin/cpp
# define              =  -DFLEXIBLE
# integrator          =  steep
# nsteps              =  5000
# emtol               =  10.0
# emstep              =  0.01
# nstcgsteep          =  100
# coulombtype         = PME
# rvdw                = 1.0
# rlist               = 1.1
# rcoulomb            = 1.1
# pme_order           = 4
# ewald_rtol          = 1e-5
# vdwtype             = shift
# ns_type             = grid
# nstlist             = 10
#
################################################################################
#
# Here's the command line:
#
# ./NAMOT_to_ffAMBER_in_GROMACS.sed $1 $2
#
# $1 = file name (including the .pdb, as I often forget to not include it)
# $2 = number of the 3' base for conversion into Dn3 (n = A,T,G,C)
# the number in $2 will automatically do the 3' and 5' conversion (keep the
# terminal hydrogens on the PO4- groups)
#
################################################################################
################################################################################
#
# The magic happens below.
#
################################################################################
################################################################################
#
# First thing first, make a backup of the original pdb file in case you goof.
#
cp $1 $1_original
#
################################################################################
#
# This section converts all of the "*" with "z" so that you're not using the
# asterisk during the editing.  Replacing with the ffAMBER-requisite
# "single-quote" (') makes the sed script more complicated than it needs to be.
#
sed 's/*/z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# The section below deletes all of the non-polar CH2 and CH hydrogen atoms from
# the nucleic acids. In GROMACS, these are mass-subsumed into the carbon atom,
# so are ignored in the toplogy.
#
#
# deletes from ADE
#
sed '/H2Az ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z ADE/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from ADE
#
# deletes from CYT
#
sed '/H2Az CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z CYT/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from CYT
#
# deletes from GUA
#
sed '/H2Az GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z GUA/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from GUA
#
# deletes from THY
#
sed '/H2Az THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/H2Bz THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/1H5z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/2H5z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H1z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H3z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
sed '/ H4z THY/d' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done deleting from THY
#
################################################################################
#
# This section changes the two nitrogen hydrogen labels to those expected by
# GROMACS.  Hn2/1, where n is the atom number in the formal labeling scheme.
#
#
# renames the NH2 hydrogen atoms for DADE
#
sed 's/HN6A/ H61/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN6B/ H62/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DADE
#
# renames the NH2 hydrogen atoms for DCYT
#
sed 's/HN4A/ H41/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN4B/ H42/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DCYT
#
# renames the NH2 hydrogen atoms for DGUA
#
sed 's/HN2A/ H21/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/HN2B/ H22/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# done renaming the NH2 hydrogen atoms for DGUA
#
################################################################################
#
# This section renames the O3' and O5' oxygen atoms from the NAMOT output
# (O5T to O5* and O3T to O3*) to a PDB format so that the terminal H atoms
# can be added on with the T/F_NA topologies.
#
#
sed 's/O5T/O5z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
sed 's/O3T/O3z/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section converts ADE, CYT, GUA, THY to DADE, DCYT, DGUA, DTHY in accord
# with the topology labels used by GROMACS for the nucleic acids.
#
#
sed 's/ADE /DADE/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/CYT /DCYT/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/GUA /DGUA/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/THY /DTHY/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section moves the column 23 chain labels to column 22 so that grompp
# can generate unique topology files for each unique chain.  As long as only
# lower-case letters are used for the chain labels (and this is the NAMOT
# default) the below moves everything and not any single-atom labels (which
# are generally all uppercase).
#
#
sed 's/ [a-z] /[a-z]  /' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# This section only replaces the FIRST nucleic acid for each chain with the F
# (5' end) labels for use with the F_NA topology.
#
# Yes, NAMOT starts its structures at the 5' end.
#
#
sed 's/DADEa   1/FADEa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa   1/FCYTa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa   1/FGUAa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa   1/FTHYa   1/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
sed 's/DADEb   1/FADEb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb   1/FCYTb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb   1/FGUAb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb   1/FTHYb   1/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
################################################################################
#
# This section changes the last base in the series to a "T" from the default
# "D" so that the topology corrects the 3' end.  Goes by units, tens, hun, thou
# and searches specifically for the pattern in question (taking care to follow
# the standard  format for base number.
#
################################################################################
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 1/a
#
sed 's/DADEa   '$2'/TADEa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa   '$2'/TCYTa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa   '$2'/TGUAa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa   '$2'/TTHYa   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1 to 9 (units)
# strand 2/b
#
sed 's/DADEb   '$2'/TADEb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb   '$2'/TCYTb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb   '$2'/TGUAb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb   '$2'/TTHYb   '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 1/a
#
sed 's/DADEa  '$2'/TADEa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa  '$2'/TCYTa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa  '$2'/TGUAa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa  '$2'/TTHYa  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 10 to 99 (tens)
# strand 2/b
#
sed 's/DADEb  '$2'/TADEb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb  '$2'/TCYTb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb  '$2'/TGUAb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb  '$2'/TTHYb  '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 1/a
#
sed 's/DADEa '$2'/TADEa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa '$2'/TCYTa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa '$2'/TGUAa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa '$2'/TTHYa '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 100 to 999 (hund)
# strand 2/b
#
sed 's/DADEb '$2'/TADEb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb '$2'/TCYTb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb '$2'/TGUAb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb '$2'/TTHYb '$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
################################################################################
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 1/a
#
sed 's/DADEa'$2'/TADEa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTa'$2'/TCYTa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAa'$2'/TGUAa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYa'$2'/TTHYa'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
# changes the 3' strand if the length is from 1000 to 9999 (thou)
# strand 2/b
#
sed 's/DADEb'$2'/TADEb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DCYTb'$2'/TCYTb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DGUAb'$2'/TGUAb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
sed 's/DTHYb'$2'/TTHYb'$2'/' $1 > $1_temp
rm $1
mv $1_temp $1
#
#
################################################################################
#
# Home stretch.  Changes all of the "z" atoms in the pdb file to * for GROMACS.
#
sed 's/z/*/' $1 > $1_temp
rm $1
cp $1_temp $1
cp $1_temp $1_postscript
rm $1_temp
#
################################################################################
#
# Questions?  Problems?  Complaints?  Better Ideas?
# Damian Allis, damian@somewhereville.com, www.somewhereville.com
#
################################################################################

chemistry.csulb.edu/ffamber
namot.lanl.gov
www.gromacs.org
en.wikipedia.org/wiki/DNA
www.rcsb.org/pdb/home/home.do
en.wikipedia.org/wiki/GROMOS
en.wikipedia.org/wiki/Thymine
en.wikipedia.org/wiki/Sed
en.wikipedia.org/wiki/Linux
en.wikipedia.org/wiki/Unix
www.apple.com/macosx