pkmukher wrote:
Hello group users,
I am trying to prepare a protein using the pdb2gmx module
of gromacs.I have stripped the hydrogens using a different
program and using a pdb file as the input.I am getting the
following error message. Please help me with your
suggestions on this.
Thank you kindly.
Opening library file
/usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat
Number of bonds was 1726, now 1723
Generating angles, dihedrals and pairs...
Before cleaning: 2697 pairs
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pgutil.c, line: 87
Fatal error:
Atom N not found in residue 1 while adding improper
So, is there an N atom in your first residue?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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