[gmx-users] pdb2gmx with more than 9999 residues

Peter C. Lai pcl at uab.edu
Tue Oct 2 08:26:13 CEST 2012

A pdb file with a resid > 9999 exceeds the proper PDB format.

You can resolvate a dry lipid bilayer using genbox fine; I don't know what 
problem you have with the solvation and minimization using that method,

You can also pdb2gmx or editconf the lipids and water separately as you 
suggested, then merge the files and run ediconf on the merged file to 
renumber the atoms.

On 2012-10-02 02:16:00PM +0800, Jernej Zidar wrote:
> Hi.
>   I'm trying to import a solvated lipid bilayer
> (cholesterol+POPC+water) I generated in CHARMM but I have a problem
> with pdb2gmx unwilling to accept the segment containing water
> molecules. It does import everything seemingly correctly, yet when one
> examines the resulting .gro file, he can see that the system does not
> accept more than 9999 residues/segment: residue 10000 becomes 1000 and
> so on.
>   Now, what can one do ammend the current situation?
>   One option would be to import only the lipid part of the system and
> then solvate it again in GROMACS, but that path is not really useful
> because it doesn't allow to fine tune the amount and location of water
> molecules. I tried this option but it doesn't work in my case as
> there's a gaping hole between the water layer and the lipids, that
> cause the minimization to essentially fail.
>   Another option would be to import the lipid and water part
> separately but this would again cause problems with atom numbering
> when both segments would be combined together.
>   Manually editing the PDB file is not an option as the PDB file has
> ~80.000 lines.
>   Any other way?
>   I'm using GROMACS 4.5.5 on Ubuntu 12.04 64-bit.
> Thanks in advance,
> Jernej
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Peter C. Lai			| University of Alabama-Birmingham
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