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.

Regards
Vasumathi 

---
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