[gmx-users] RE: opls

[Dongsheng Zhang]

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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