VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Fri May 30 2014 - 15:33:52 CDT

If it's all one molecule you could still potentially work around it... just restart your numbering from 1 at the 10,000th residue and make it a fresh segment, then manually patch the backbones back together (PRES LIG for a protein, if I recall correctly)?

One concern: how is it numbered in the PDB file itself? I believe the PDB format only allows four characters for residue numbers.

 
 
Tristan Croll
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Queensland University of Technology
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> On 30 May 2014, at 11:52 pm, "Josh Vermaas" <vermaas2_at_illinois.edu> wrote:
>
> 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 havenīt 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
>