From: Josh Vermaas (
Date: Thu May 29 2014 - 08:46:30 CDT

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,

-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
> havenĀ“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