[gmx-users] PDB2GMX Not Using .itp File

Gromacs Newbie gromacs_newbie at yahoo.com
Tue Jul 13 20:30:22 CEST 2004

Hi All,

I downloaded the topology for cholesterol (.pdb and
.itp) off Gromacs and I tried to process it with the
pdb2gmx command: 

pdb2gmx -f cholesterol.pdb -i cholesterol.itp -o
ch.gro -p ch.top

but it gives me the following error:

Warning: 'CHOL' not found in residue topology
database, trying to use 'CH3OH'
Fatal error: Atom C1 in residue CH3OH 1 not found in
rtp entry with 3 atoms
             while sorting atoms

>From my understanding CHOL should be defined in
cholesterol.itp but it doesn't seem to be finding the

Thanks in advance.


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