Re: PBB File Format/Setup for PBC

From: johan strumpfer (
Date: Fri Aug 19 2011 - 17:41:04 CDT

Hi Anna,

That is standard practice for vmd's solvate plugin (it happens even
when you use a plain water solvent). The segids and chain do not
affect the simulation at all. All the relevant information to
calculate the energy is in the psf file (i.e., atom types, charges,
which atoms are bonded, what angle, dihedral and impropers terms are
defined). The segid and chain do not play a role in the dynamics


Johan Strumpfer:
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Fri, Aug 19, 2011 at 8:24 AM, Anna James <> wrote:
> Just before heating and equilibrating my protein.I wanted to be sure of some
> points about the PDB file data:
> I used the VMD to solvate my protein with a non standard solvent box which
> had more than 15000 residues of (Methanol+Water Molecules)combined system.
> 1. My Protein is represented by a particular SEGID
> 2. Due to the format limit in PDB files of 9999 residues for a particular
> segid, I had to split my solvent into three different segids,There are three
> different chains as well:
> WT1 for water residues ( 1-9999);Chain A
> +
> WT2 for water residues ( 1-3456);Chain B
> +
> MT1 for methanol residues (1-6780): Chain C
> My doubt is that does the classification based on the segids and chain
> affect the simulation in anyway ?
> Should the whole solvent be considered as having one segid or the solvent
> constituents can have different segids?
> Does the naming based on chain name have anything to do with the behavious
> of anything as solvent molecules or protein molecule?
> I used the above PDB file to also generate a PSF file for it.Does PSF file
> depend at all on the segids and chain name ?
> Any advice on above will be of great help and clear my last hurdle
> Anna James Vaughan
> Leeds University

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