[gmx-users] pdb2gmx

herbst at fhi-berlin.mpg.de herbst at fhi-berlin.mpg.de
Thu Jun 10 12:28:15 CEST 2004


I tried to create a .top file from a .pdb file for a small molecule (32
atoms) with pdb2gmx.:

pdb2gmx -f 81 -o 81 -p 81

For it is not a standard amino acid, I added the structure of the molecule
to ffgmx.rtp named 81, but pdb2gmx does not recognize the molecule.  The
same error appears as before I added the molecule structure to ffgmx.rtp:

Fatal error: Residue '2' not found in residue topology database

Any ideas?

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