On 9/03/2012 8:50 AM, MPID wrote:
I am running g_helix on a run involving a 37 residue protein in the charmm
force field. It has two long alpha helical segments. I have tried running
g_helix with many different variations of commands and getting rid of PBC
effects, but I always get the same error:
Checking group System
There are 37 residues
There are 0 complete backbone residues (from 0 to 524)
-------------------------------------------------------
Program g_helix, VERSION 4.5.5
Source code file: /home/shared/installers/gromacs-4.5.5/src/tools/hxprops.c,
line: 388
Fatal error:
rnr==0
--------------------------------------------------------
Is rnr the number of peptide residues, or the number that are helical? In
either case, nothing I do can seem to make it different from 0.
The code is
fprintf(stderr,"There are %d complete backbone residues (from %d to
%d)\n",
rnr,bb[i0].resno,bb[i1].resno);
if (rnr==0)
gmx_fatal(FARGS,"rnr==0");
So zero complete backbone residues were found for some reason, and the
person who wrote g_helix was cryptic about it.
The code relies on finding atoms named "N", "H", "CA", "C", "O" in the
same residue.
Mark
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