VMD-L Mailing List

From: Shahee Islam (shaheeislam726_at_gmail.com)
Date: Mon Jan 29 2018 - 02:34:29 CST

REMARKS original generated structure x-plor psf file^M
 REMARKS 6 patches were applied to the molecule.^M
 REMARKS topology prac-cg_autopsf-temp.top ^M
 REMARKS segment P1 { first NTER; last CTER; auto none }^M
 REMARKS patch NTER P1:1 ^M
 REMARKS patch CTER P1:129 ^M
these above lines are mentionet at the top of the psf file.but in the bond
section of psf there is no mention of the above bonds.but in the autopsf
log file these below lines are mention
Applying patch: DISU Prot:15 Prot:278
Applying patch: DISU Prot:69 Prot:252
Applying patch: DISU Prot:171 Prot:205
Applying patch: DISU Prot:147 Prot:179

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
>>
>
>