[gmx-users] Prot_prep_problem

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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