Re: [gmx-users] how to modify opls force field

[zjim]

Hi Zhang
I have also modified opsl force field as the way which you mention.I think what you have done is OK! As for your problem, I think it is caused by the modified residue "MSO" is not included in the file "/share/top/aminoacids.dat",and the programe does not know it is a amino acid. you may add the name "MSO" to the file and try again.good luck!

  Jin ming

> Dear Gromacs users,
> 
> I tried to use opsl force field to simulation a pentapeptide solution.
> The residue in my pentapeptide is very similar to Methionine. The only
> difference is the atom between CG and CE is O, not S (in Methionine).
> Because this residue is not included in ffoplsaa.rtp, I made a new .rtp
> file by adding a new residue. I named it MSO. The atom type for O in MSO
> is opsl_999 (I treated it as opsl_180, O in the dialkyl ether). I also
> modified ffoplsaa.atp, ffoplsaabon.itp, ffoplsaa.hdb, ffoplsaa.itp and
> ffoplsaanb.itp by adding new parameters. In short, I made my own force
> field for my pentapeptide, and I gave it a new name. However, when I
> tried to use pdb2gmx to convert my pdb file, I got the error message as
> follows:
> 
> No N- or C-terminus found: this chain appears to contain no protein
> Fatal error: Atom -C not found in residue MSO1 while adding hydrogens
> 
> 
> Because I just added more parameters to opsl force field to get my own
> force field, I think my new force field should work for Methionine
> pentapeptide, so I changeed my pdb file to Methionine pentapeptide. When
> I tried pdb2gmx, it worked fine.
> 
> Another test I have done is I modified ffoplsaa.rtp by changing the
> definition of MET, namely I changed SD to OD in [MET] section (and
> changed other things accordingly). I also changed SD to OD in MET
> section in the file ffoplsaa.hdb. Then I tried pdb2gmx, it worked as
> well.
> 
> Could anyone tell me what's wrong with the modification by adding one
> more residue type? Any helps are highly appreciated. If you need more
> information, please let me know.
> 
> 
> Thanks in advance!
> 
> 
> 
> -- 
> Dongsheng Zhang 
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