[gmx-users] RE: opls
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Sat Sep 2 17:08:18 CEST 2006
Hello,
I believe this question has been asked several times. It is true that
ffoplsaabon.itp misses some parameters for dihedral for the capped
residues (ACE NAC). I think you can add some estimated values to the
ffoplsaabon.itp, or ignore the warnings.
All the best!
Donnsheng
On Sat, 2006-09-02 at 14:36 +0200, singh wrote:
>
>
>
> Hi,
> I have checked both the files. These lines corresponds to following
> dihedrals in my topology
>
> Dihedral (1-5-7-9)
> 1 opls_135 1 ACE CH3 1 -0.18 12.011 ; qtot
> -0.18
> 5 opls_235 1 ACE C 2 0.5 12.011 ; qtot
> 0.5
> 7 opls_238 2 PHE N 3 -0.5 14.0067 ; qtot
> -0.5
> 9 opls_224B 2 PHE CA 3 0.14 12.011 ; qtot
> -0.06
>
> And (81-88-90-92)
> 81 opls_224B 6 SER CA 30 0.14 12.011 ;
> qtot -0.06
> 88 opls_235 6 SER C 33 0.5 12.011 ;
> qtot 0.5
> 90 opls_238 7 NAC N 34 -0.5 14.0067 ;
> qtot -0.5
> 92 opls_242 7 NAC CH3 35 0.02 12.011 ;
> qtot -0.18
> In rtp file all the atomtypes are there in corresponding residues however in
> ffoplsaabon.itp, I could not find an entry in dihedral types for these
> dihedrals.
>
> Regards,
> Gurpreet Singh
>
>
>
>
>
>
>
>
> Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp
>
> Yang Ye
>
> singh wrote:
> >
> > Dear Users,
> >
> > I am trying to simulate a capped pentapeptide using OPLS force field.
> > Pdb2gmx runs successfully , however grompp gives following warnings
> >
> > WARNING 1 [file "topol.top", line 632]:
> >
> > No default Ryckaert-Bell. types, using zeroes
> >
> > WARNING 2 [file "topol.top", line 857]:
> >
> > No default Ryckaert-Bell. types, using zeroes
> >
> >
> >
> > How should I proceed if these parameters are missing in OPLS.
> >
> > The topology and gro files are attached herewith
> >
> >
> >
> > Regards,
> >
> > Gurpreet
> >
> > -------------------------------------------------
> >
> > University of Dortmund
> > Department of Chemistry
> > Physical Chemistry I - Biophysical Chemistry
> > Otto-Hahn Str. 6
> > D-44227 Dortmund
> > Germany
> >
> > Office: C1-06 room 176
> > Phone: +49 231 755 3916
> >
>
>
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