[gmx-users] NH2 IN CTERMINAL

shahrbanoo karbalaee shahrbanoo at gmail.com
Tue Sep 30 14:07:28 CEST 2008

Dear justin
In my simulation with ff53a5 when I do this command  pdb2gmx  -f
name.pdb  -ter  -ignh -water spce .I find this error .C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 142, now 139
Generating angles, dihedrals and pairs...
Before cleaning: 210 pairs

Program pdb2gmx, VERSION 3.3.2
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 14 while adding improper

how can resolve this problem?

best regards

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