[gmx-users] pdb2gmx on KcsA

Kaasi Sridhara research.gromacs at gmail.com
Sun Dec 25 01:58:19 CET 2005

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
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)
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......
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