[gmx-users] tfe and gromos9653a

shahrbanoo karbalaee shahrbanoo at gmail.com
Thu Aug 21 18:49:37 CEST 2008

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
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



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