VMD-L Mailing List
From: Vasumathi Velachi (vas_at_fc.up.pt)
Date: Fri May 30 2014 - 04:25:01 CDT
Dear Josh Vermaas and Subbarao
It is single molecule. The problem is, it reads upto 9999 residue and
leave the other atoms.
--- Vasumathi Velachi Em 2014-05-29 14:46, Josh Vermaas escreveu: > Hi Vasumathi, > > I don't think that psfgen properly handles segments containing more > than 10,000 residues. What I've done in the past is to fragment the > input pdb into smaller chunks and use psfgen as usual on these new > smaller segments. Just to be clear, it isn't a single molecule with > more than 10,000 residues, right? Its some assembly/solvation box > that > is too big, right? > > -Josh Vermaas > > On 5/29/14, 6:13 AM, Vasumathi Velachi wrote: >> >> Dear All >> I have to create a psf file which will be used for solvating the >> system in VMD. Normally I use psfgen for generating psf file. So far i >> haven´t met any problem but now >> I am having a problem in reading pdb file which has more than 10 >> thousand residues. Is there anyway to read a pdb file(more than 10 >> thousand residues) in psfgen? >> Thanking you in advance