[gmx-users] RE: opls

[singh]

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
>
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