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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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