Hi Shima, It seems like this residue is not parameterized for the force field you want to use. Maybe check http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks if you can find it under a different name. If not, have a look at http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.
Cheers, Felix Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Shima Arasteh Gesendet: Donnerstag, 12. April 2012 09:43 An: Discussion list for GROMACS users Betreff: [gmx-users] Residue 'FOR' not found in residue topology database Dear Gromacs friends, I attached my .pdb file in this message, as you see, I have formyl residue in it. I'd like to get a .gro output of it by using this commands, but getting the fatal error: # pdb2gmx -f glc.pdb -o glc.gro -ignh -ter -water spc Fatal error: Residue 'FOR' not found in residue topology database How can I solve this problem? Thanks , Shima
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