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
ethanediol.tgz
Description: application/compressed-tar
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