Compiling And Running GAMESS-US (1 May 2013(R1)) On 64-bit Ubuntu 12.X/13.X In SMP Mode

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

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Bash Script For Generating 3D Potential Energy Surface Scan Input Files


The above scripts were made to overcome some of the potential energy surface (PES) scan limitations (well, design issues I’d rather not design around) in GAMESS and Gaussian. The intent of the scripts are to:

a) take a molecular input file from some quantum chemical code

b) align the molecule such that the surface you want to perform the PES scan across is aligned in the XY, YZ, or XZ planes

c) define the atom/molecule you want to scan with (such as a cation) in variable form in the input file template

d) define the grid size you want to perform the scan with (how fine a mesh)

e) generate the input files

and finally,

f) write out a command line script in a format that leaves for little post-processing for both the calculation and the analysis.

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Synthetic, Structural And Theoretical Investigations Of Alkali Metal Germanium Hydrides – Contact Molecules And Separated Ions

In press, available from Chemistry – A European Journal. This is a paper a year or so in the making that, had I started it a year from now, would have taken a very different route. Much of the work I’ve done in neutron and terahertz spectroscopy has demonstrated that the inclusion of the crystal environment in quantum chemical treatments of solid-state systems is the key to interpreting the data (makes sense). This paper examines the unusual orientation of the [GeH3] anion in two crown ether complexes with potassium (K+) and rubidium (Rb+) cations. The crystal cells of these two complexes are far larger than computational resources would handle now (and definitely when the project started), but they’d be easily handled on better equipment (such as an 8-processor box with a terabyte or so of scratch space). The isolated molecule calculations (Dr. Alex Granovsky’s PC-GAMESS version with basis sets from EMSL) demonstrate that the potential energy surfaces corresponding to anion orientations in the vicinity of only the solvated cations is shallow (at best) and that any moderate collection of electrostatic interactions (such as those in the crystal cell) may be enough to stabilize the unexpected anion orientation. It is also of interest to note that the [GeH3] anion prefers to bind to the K/Rb cations by the hydrogens (which we refer to as “inverted”) and NOT the germanium anionic lone pair (the traditional, van’t Hoff arrangement, all of those calculations being performed at B3LYP/6-311G(d,p) and MP2/6-311G(d,p) levels of theory with LANL2DZ ECPs for the K and Rb). This “oddity” was considered previously by the great Paul v. R. Schleyer and coworkers for a similar Na-SiH3 system some time back (Angew. Chem. 1994, 106, 221-223). This project will hopefully be revisited with solid-state density functional theory to see just how the crystal interactions combine to impose the non-traditional [GeH3] binding orientation.

karin geh3

W. Teng, D. G. Allis and K. Ruhlandt-Senge

Abstract: The preparation of a series of crown ether-ligated alkali metal (M = K, Rb, Cs) germyl derivatives M(crown ether)GeH3 via hydrolysis of the respective tris(trimethylsilyl)germanides is reported. Depending on the alkali metal and the crown ether diameter, the hydrides display either contact molecules or separated ions in the solid state, providing a unique structural insight into the geometry of the obscure GeH3 anion.

Germyl derivatives displaying M-Ge bonds in the solid state are of the general formula M([18]crown-6)(thf)GeH3 with M = K, 1; M = Rb, 4. Interestingly, the lone pair at germanium is not pointed towards the alkali metal, rather two of the three hydrides are approaching the alkali metal center to display M-H interactions.

Separated ions display alkali metal cations bound to two crown ethers in a sandwich-type arrangement and non-coordinated GeH3 anions to afford complexes of the type [M(crown ether)2][GeH3] with M = K, crown ether = [15]crown-5, 2; M = K, crown ether = [12]crown-4, 3 and M = Cs, crown ether = [18]crown-6, 5.

The highly reactive germyl derivatives were characterized using X-ray crystallography, 1H and 13C NMR, and IR spectroscopy. Density functional theory (DFT) and Second-Order Moeller-Plesset perturbation theory (MP2) calculations were performed to analyze the geometry of the GeH3 anion in the contact molecules 1 and 4.’t_Hoff

Extension Of The Single Amino Acid Chelate Concept (SAAC) To Bifunctional Biotin Analogues For Complexation Of The M(CO)3+1 Core (M = Tc And Re): Syntheses, Characterization, Biotinidase Stability And Avidin Binding

In press, available from the journal Bioconjugate Chemistry. The modeling study for the avidinbiotin structure and the biotin derivatives were completed with the molecular dynamics program NAMD on a Dual G4/450 loaned to me from Apple for development work, for which I am grateful (I’ve performed molecular dynamics simulations with the Walrus). I did manage to smoke the motherboard during this experience, for which I apologize. Given the state of the machine after the autopsy, I’m hoping no one (especially Eric Zelman!) asks for it back, even when I’m 64.

I made mention of the reasons for some of this work in an interview I did for, completely unrelate to the other content, in case anyone wants some background.

Shelly James, Kevin P. Maresca, Damian G. Allis, John F. Valliant, William Eckelman, John W. Babich, and Jon Zubieta

Abstract: Biotin and avidin form one of the most stable complexes known (KD = 10-15M-1) making this pairing attractive for a variety of biomedical applications including targeted radiotherapy. In this application one of the pair is attached to a targeting molecule while the other is subsequently used to deliver a radionuclide for imaging and/or therapeutic applications. Recently we reported a new single amino acid chelate (SAAC) capable of forming robust complexes with Tc(CO)3 or Re(CO)3 cores. We describe here the application of SAAC analogs for the development of a series of novel radiolabeled biotin derivatives capable of forming robust complexes with both Tc and Re. Compounds were prepared through varying modification of the free carboxylic acid group of biotin. Each 99mTc complex of SAAC-biotin was studied for their ability to bind avidin, susceptibility to biotinidase and specificity for avidin in an in vivo avidin-containing tumor model. The radiochemical stability of the 99mTc(CO)3 complexes was also investigated by challenging each 99mTc-complex with large molar excesses of cysteine and histidine at elevated temperature. All compounds were radiochemically stable for greater than 24 hours at elevated temperature in the presence of histidine and cysteine. Both [99mTc(CO)3(L6)]+1 [TcL6; L6 = biotinyl- amido- propyl- N,N- (dipicolyl)- amine] and [99mTc(CO)3(L12a)]+1 (TcL12; L12 = N,N-(dipicolyl)- biotin- amido- Boc- lysine; TcL12a; L12a = N,N- (dipicolyl)- biotin- amide- lysine) readily bound to avidin whereas [99mTc(CO)3(L9)]+1 [TcL9; L9 = N,N- (dipicolyl)- biotin- amine] demonstrated minimal specific binding. TcL6 and TcL9 were resistant to biotinidase cleavage while TcL12a, which contains a lysine linkage, was rapidly cleaved. The highest uptake in an in vivo avidin tumor model was exhibited by TcL6, followed by TcL9 and TcL12a, respectively. This is likely the result of both intact binding to avidin and resistance to circulating biotinidase. Ligand L6 is the first SAAC analogue of biotin to demonstrate potential as a radiolabeled targeting vector of biotin capable of forming robust radiochemical complexes with both 99mTc and rhenium radionuclides.Computational simulations were performed to assess biotin-derivative accommodation within the binding site of the avidin. These calculations demonstrate that deformation of the surface domain of the binding pocket can occur to accommodate the transition metal-biotin derivatives with negligible changes to the inner-β-barrel, the region most responsible for binding and retaining biotin and its derivatives.

P.S. This publication is also of some use for explaining the series of images on the current departmental brochure for the Syracuse U. Chemistry Department. Steric interactions affect the local geometries of protein binding pockets. And a good thing, too.

Click on the image for a larger version.

Everything You Need To Set Up PC-GAMESS On A(n) SMP System

The following is a step-by-step guide to getting PC-GAMESS 6.4 (perhaps prior. I’m not inclined to check, but would appreciate a confirmation) running on a(n) SMP (that’s Symmetric MultiProcessing (useless trivia), a single motherboard with multiple processors) system. All of the websites describing what’s below are less… obvious than I would like, especially concerning the infamous .pg file for SMP machines. What’s below is specifically geared for a dual-core/dual-board (four processor) system, but is easily changed to other SMP cases.

1. Obtain the most recent (6.4 as of this posting) version of PC-GAMESS from the good Dr. Alex Granovsky.

2. After extracting the contents of the downloaded .exe file, you’ll notice the wmpi1_3.exe file. Double click to install this program, blindly saying yes to everything it asks.

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Using External Basis Sets In GAMESS-US, Running Mixed Basis Set Calculations With Z-Matrix Inputs

The parameterization of the new nanoENGINEER-1 simulator is being performed for molecules containing H through Cl at the B3LYP/6-31+G(d,p) level of theory. Unfortunately, the 6-31+G(d,p) basis set is not available for the 4th row elements (Ga,Ge,As,Se,Br), meaning an alternate basis set is required (for the 4th row, that is). In GAMESS-US, this is simple if the input files are in Cartesian format. This same approach cannot be used in Z-matrix input formats. A (maybe THE only) way to call mixed basis sets for Z-matrices in GAMESS-US is provided here. The procedure involves making an external basis set file with the required basis sets, changing the $BASIS control to read the external file, and modifying rungms to read the external basis set file.

Below is a sample input file. The only noteworthy differences between it and any other input file are (a) the $BASIS line, which tells GAMESS-US to use the external file (EXTFIL=.TRUE.) and (b) the call to use external basis sets named STO2GBAS. In this external file, you can have multiple groups of elements and basis sets, but not multiple basis set types for the SAME ELEMENT in the same group (so far as I know at the moment). This means that the external basis set example file I have available here has Hydrogen (H) and F (Fluorine) STO-2G (STO2GBAS) and 3-21G (321GBASI) basis set groups, but that you CANNOT call the STO2GBAS Hydrogen basis set and 321GBASI Fluorine basis set.

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An (Old) Automatic PC-GAMESS Batch Script

From a prior version of the site…

This batch script acts similar to GQueue for MacGamess, with the exception that you can’t add files after the .bat file has been implemented (run). This new version automatically goes through a directory containing PC-GAMESS input (.inp) files and runs them without having to specify each name in a long batch file. all one has to do is double-click on the rungamess.bat file from a window and it will automatically start the command prompt and program.

There is a limit to the use of the FOR command in DOS that I’ve not yet found a way to overcome, so the actual batch script is divided into two files. The first, rungamess.bat, contains the code that collects the .inp files and passes each name sequentially to execute.bat, the file that actually starts PC-GAMESS and runs the calculation. While an annoyance to have two files, once they are placed you never have to touch them again (unless you want to pass parallel calculation parameters to the executable, which are done in the execute.bat file).

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(Why Did) OpenSuse (Do That?), GAMESS-US, And libg2c

The OpenSuse 10.0 CD set, still the only distro to install cleanly on my Precision M70, DOESN’T contain lots of useful developmental software and libraries some of ye olde quantum chemical codes need to run. This is painfully apparent to those who have downloaded the pre-compiled GAMESS-US code and found it not to do run (and what’s with the OSX in the README?) because of missing libg2c files. Yes, even real tech geeks are too lazy to make some days. That may have come out wrong.

If your goal is just to get the program running, the quick fix is to feed your machine just the libraries (a proper compilation or, uh, more complete Linux installation would also work, but that’s beyond the scope of this blog). This involves the following:

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