VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri May 30 2014 - 07:08:27 CDT

Hi Vasumathi,

I'm using the chemical definition of molecule. Are all those 10,000
residues bonded together? Or is it like 10,000 different water
molecules? If its the first case, I'm curious as to what it is, but if
its the second, just fragment it into different pieces and put each
piece in a different segment.
-Josh Vermaas

On 05/30/2014 05:25 AM, Vasumathi Velachi wrote:
> 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
>