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