PBB File Format/Setup for PBC

From: Anna James (annajamesmatrix_at_hotmail.com)
Date: Fri Aug 19 2011 - 07:24:11 CDT

Just before heating and equilibrating my protein.I wanted to be sure of some points about the PDB file data:
 used the VMD to solvate my protein with a non standard solvent box
which had more than 15000 residues of (Methanol+Water Molecules)combined

1. My Protein is represented by a particular SEGID
 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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