[gmx-users] Prot_prep_problem

pkmukher pkmukher at olemiss.edu
Thu Apr 5 16:01:24 CEST 2007

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.

Select the Force Field:
 0: GROMOS96 43a1 force field 
 1: GROMOS96 43b1 vacuum force field
 2: GROMOS96 43a2 force field (improved alkane dihedrals)
 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 
 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 
 6: OPLS-AA/L all-atom force field (2001 aminoacid
 7: [DEPRECATED] Gromacs force field (see manual)
 8: [DEPRECATED] Gromacs force field with hydrogens for NMR
 9: Encad all-atom force field, using scaled-down vacuum
10: Encad all-atom force field, using full solvent charges  
Opening library file
Opening library file
Reading 1YSI_orient_chop2_protein_noH.pdb...
Read 1307 atoms
Opening library file
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 163 residues
with 1307 atoms

  chain  #res #atoms
  1 'A'   163   1307  

All occupancies are one
Opening library file
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file
Residue 96
Sorting it all out...
Opening library file
Opening library file
Opening library file

Back Off! I just backed up j.top to ./#j.top.1#
Processing chain 1 'A' (1307 atoms, 163 residues)
There are 247 donors and 258 acceptors
There are 294 hydrogen bonds
Will use HISB for residue 77
Will use HISB for residue 141
Checking for duplicate atoms....
Opening library file
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 163 residues with 1693 atoms
Making bonds...
Opening library file
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


"Torture You.... Yeah, That's a Good Idea, I Like That."
(Pulp Fiction)

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi

Cell   - 662 380 0146
Office - 662 915 1286 

More information about the gromacs.org_gmx-users mailing list