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
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