[gmx-users] Trouble using Encad in gmx-3.3

Leonardo Sepulveda Durán leonardosepulveda at gmail.com
Sat Oct 15 06:19:18 CEST 2005


I was trying to test Encad Force Field. I used

pdb2gmx -f 1ENH.pdb

After choosing force field 10, this error appears

Opening library file
Number of bonds was 953, now 953
Generating angles, dihedrals and pairs...
Before cleaning: 2494 pairs
Program pdb2gmx, VERSION 3.3
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 2 while adding improper


I used other Protein and the same happens, but in a different residue. Both
have in common being a Proline residue. I am not sure if this is a bug or i
am doing something wrong.

By the way, As I have read from levitt's protocols, ENCAD is used with ATOM
based nb interactions, and they use their own cutoff scheme, very similar to
B.BrooKs's Force shifted spherical cutoff. Is it posible to use that
protocols? How can be selected in a mdp file? I have not found info
regarding that.


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