[gmx-users] tfe and gromos9653a

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 21 20:10:06 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
> I guess I did right.I add in my topoly file tfe   in part of dehedrals
> " gd_24".(from your edit  in  dmso topolgy  last another mail)and I
> could minimize. what do you think this adding ?.any way thank you for
> every thing.now about my peptide I have this error .(in c terminal
> peptide   is amidated) and in this force field ffG53a5,I tried to edit
> this error (refine pdb file and ...). but  didnot.(the 14 residue is
> phe)

I don't know, does gd_24 correspond to the missing dihedral involving your atoms?

> 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
> -------------------------------------------------------

Without seeing your command line, I have absolutely no idea what you've done. 
Please, take my advice (that I've given about ten times) - post command lines if 
you post errors.  You probably didn't specify -ignh, but that's just a guess 
because I can't get into your head!



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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