[gmx-users] pdb2gmx on KcsA

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Dec 25 10:15:10 CET 2005

Hi Kaasi,

The error message indicates that some residues are incomplete. You have to
first complete these residues and also check for residues which are missing
entirely, which you should add, as was done for the work you're trying to

By the way, I noticed that you tried to use the gmx force field, which is a
bad choice. Didn't the authors state which force field they used? Gromos

Good luck,


On 12/25/05, Kaasi Sridhara <research.gromacs at gmail.com> wrote:
> Hi Everyone,
> This is the first time I am working on proteins in lipid bilayer.
> I downloaded 1bl8.pdb( KcsA potassium channel) and tried to do pdb2gmx on
> this pdb file.
> I got the following error:
> Fatal Error : Atom CZ not found in residue ARG 95 while adding hydrogens.
> I used Gromacs Forcefield (4 option from 0-5).
> I tried to look into the archives, I could find only one thread, but which
> did not finally solve the problem.
> ---------
> About the pdb file, the residue numbering starts from 23 .
> My aim is to replicate the results obtained from the following journal
> Simulations of Ion Permeation Through a Potassium Channel: Molecular
> Dynamics of KcsA in a Phospholipid Bilayer by Shrivastava and Sansom.
> -------
> They described a bit about the procedure, but I am not favourable with
> what they were talking.
> ----I am just adding directly the lines from the journal----
> ""The protein structure was that in PDB file 1bl8, with the modification
> that
> atoms for all side chains were included. The "missing" residues were added
> by building in stereochemically preferred conformers. Although not
> present in the x-ray structure, an inter-subunit salt bridge (D80 to R89)
> was
> formed during the early stages of the simulations. Note that residues 1–22
> and 120–160 are missing from this model, which therefore represents the
> core channel-forming domain of the protein.""
> ___________
> Did anyone tried to work on this problem earlier, or can anyone suggest
> how to deal with this problem of adding missing residues.
> My problem now is to form a force-field file for this protein.
> Thanks a lot, and Wish you all a very happy festive mood......
> -Kaasi.
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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