VMD-L Mailing List

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jan 29 2018 - 02:27:09 CST

Hello Shahee,

Check your psf file. If at all any disulfide patch exist, it should be
written in the psf itself.

On Mon, Jan 29, 2018 at 1:11 PM, Shahee Islam <shaheeislam726_at_gmail.com>
wrote:

> in this case from the pdb file atfrirst i found the sulfide containig bead
> and then mention them in the disufide patch command.Please help me to solve
> this problem.
>
> Thanking you
> Shahee Islam
> university of calcutta
> department of chemistry
>
> On Mon, Jan 29, 2018 at 11:31 AM, Shahee Islam <shaheeislam726_at_gmail.com>
> wrote:
>
>> Hi
>> I have made coarse grained protein according to residue base coarse
>> grained tutorial,after that generate psf using vmd auto psf plugin.There
>> are disulfide bond,which i generate using patching disulfide bond.But the
>> problem is, the disulfide bonds are not showing in vmd.
>> in autopsf.log file these lines are present:
>> Applying patch: DISU Prot:15 Prot:278
>> Applying patch: DISU Prot:69 Prot:252
>> Applying patch: DISU Prot:147 Prot:179
>> Applying patch: DISU Prot:171 Prot:205
>>
>
> 

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275