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