[gmx-users] Fatal Equilibration Errors
Nancy
nancy5villa at gmail.com
Thu Aug 13 02:47:33 CEST 2009
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 <brucedray at yahoo.com> wrote:
> On Sunday, August 9, 2009 at 4:32:19 PM, Nancy <nancy5villa at 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
>
>
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