[gmx-users] g_helix problem

Laercio Pol Fachin laercio_pf at yahoo.com.br
Tue Sep 14 15:08:39 CEST 2010

Dear Gromacs Users:

I have a problem when I try to run g_helix in Gromacs 4.0.5.

I have two systems, each one containing a peptide, both with the same number of aminoacids; however, in one of them, most of the AA residues are not usual (in fact, they are post-translationally modified; thus, to run the MD simulations, I modified ffG43a1.rtp - aminoacids.dat - ffG43a1.hdb, to include its parameters).

Both simulations worked fine! When I try to run g_helix in the first run (with common AAs), everything goes fine:
There are 15 residues
There are 13 complete backbone residues (from 2 to 14)

However, when I do it in the other simulation, it gives me such error:
There are 15 residues
There are 0 complete backbone residues (from 0 to 136679032)

Program g_helix, VERSION 4.0.5
Source code file: hxprops.c, line: 389

Fatal error:

How can I solve this puzzle?

Thanks in advance,
Laércio Pol-Fachin

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