Hello, In an earlier message, it was stated that topolbuild generated topologies with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the only files in the "dat/gromacs" directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-AA force field used?
Thank you. Nancy On Mon, Aug 10, 2009 at 6:22 PM, Bruce D. Ray <bruced...@yahoo.com> wrote: > On Sunday, August 9, 2009 at 4:32:19 PM, Nancy <nancy5vi...@gmail.com> > wrote: > > > I obtained the ethylene glycol (1,2-ethanediol) structure from the URL: > > http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb > > > > I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF > > Chimera (http://www.cgl.ucsf.edu/chimera/). > > > > I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the > topologies: > > > > $ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir > .../topolbuild1_2_2/dat/gromacs -ff gmx53a6 > > > > which outputs the files: > > > > ethanediol.gro > > ethanediol.log > > ethanediolMOL.mol2 > > ethanediol.top > > ffethanediol.itp > > posreethanediol.itp > > > > I modified the "ffethanediol.itp" file to read: > > > > ======================================= > > #define _FF_GROMOS96 > > #define _FF_GROMOS53A6 > > #define _FF_USER > > > > [ defaults ] > > ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > > 1 1 no 1.0 1.0 > > > > #include "ffG53a6nb.itp" > > ======================================= > > > > The lack of hydrogen bonds between the solute and solvent molecules was > > due to the lack of charges in the generated topology file > "ethanediol.top". > > So I changed the "atoms" section of the topology file (the original > topology > > file is at the end of this message), and this causes hydrogen bonds > between the > > solute and solvent in numbers comparable to that between the solvent > molecules. > > > > ======================================= > > [ atoms ] > > ; nr type resnr residu atom cgnr charge mass > > 1 CH2 1 EDO C1 1 0.17600 14.02700 > ; 0.0000000 > > 2 OA 1 EDO O1 1 -0.5740 15.99940 > ; 0.0000000 > > 3 H 1 EDO HO1 1 0.39800 1.00800 > ; 0.0000000 > > 4 CH2 1 EDO C2 2 0.17600 14.02700 > ; 0.0000000 > > 5 OA 1 EDO O2 2 -0.5740 15.99940 > ; 0.0000000 > > 6 H 1 EDO HO2 2 0.39800 1.00800 > ; 0.0000000 > > ; total molecule charge = 0.0000000 > > ======================================= > > > > I obtained the charge values from the methanol tutoral included with > Gromacs > > (.../share/gromacs/tutor/methanol/methanol.itp). I then enlarge the > box and solvate the molecule: > > I used a mol2 file that I generated from a sy2 file downloaded from NCI by > first > running the file through dos2unix then replacing the 0 in the residue > number > column with 1 EDO so that I had both a correct residue number column with a > residue name column. The NCI data was missing the residue name column. I > then > read the mol2 file that resulted into UCSF Chimera and used it to generate > gasteiger > charges for ethylene glycol. Chimera wrote the following mol2 file as a > result: > > @<TRIPOS>MOLECULE > EDO > 10 9 1 0 0 > SMALL > AMBER99 > > > @<TRIPOS>ATOM > 1 O1 0.0000 0.0000 0.0000 O.3 1 EDO > -0.3940 > 2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO > 0.0662 > 3 C2 -1.7400 1.1400 -1.1400 C.3 1 EDO > 0.0662 > 4 O2 -2.5200 1.2800 0.0200 O.3 1 EDO > -0.3940 > 5 H1 0.5196 -0.8024 0.0879 H 1 EDO > 0.2102 > 6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO > 0.0588 > 7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO > 0.0588 > 8 H4 -2.3721 1.1133 -2.0029 H 1 EDO > 0.0588 > 9 H5 -1.0696 1.9696 -1.2252 H 1 EDO > 0.0588 > 10 H6 -3.0271 2.0935 -0.0316 H 1 EDO > 0.2102 > @<TRIPOS>BOND > 1 1 5 1 > 2 1 2 1 > 3 2 7 1 > 4 2 6 1 > 5 2 3 1 > 6 3 9 1 > 7 3 8 1 > 8 3 4 1 > 9 4 10 1 > @<TRIPOS>SUBSTRUCTURE > 1 EDO 2 RESIDUE 4 A EDO 0 ROOT > > > I processed this with topolbuild 1.3 and generated topologies with gromacs > 53a6 and with opls-aa as the force fields. I am attaching the results to > this > as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa > atom > types selected by topolbuld 1.3 have characteristic atom type charges > charges > of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to > oxygens, > +0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the > carbons. The comparison to the gasteiger charges Chimera assigned to these > atoms is interesting. The opls-aa topology generated also assigns to the > O1-C1-C2-O2 dihedral the diol constants found as a special define in > ffoplsaabon.itp > > {snipped} > > > The ethylene glycol lacks explicit non-polar hydrogens; is that normal > for this type of system, > > force field (based on GROMOS96 53a6) and SPC/E water model? > > The 53a6 force field is a united atoms model force field and incorporates > non-polar > hydrogens in the parameters of the carbons to which they are bound. If you > want > to treat the non-polar hydrogens separately from the carbons to which they > are > bound, you will need to use an all atoms force field such as opls-aa for > which I > have included the parameters in the attached tarred and gzipped file, > ethanediol.tgz > > I hope this is useful. > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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