VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Jan 29 2018 - 13:06:34 CST

I'm 99% certain that autopsf is trying to apply the atomic DISU patch, which deletes hydrogens and forms the bond between sulfurs that have a specific name, and you are missing those atoms. Looking at the martini topology file that comes with the residue-based coarse-graining tutorial, it looks like you could call the patches explicitly if you script it yourself:

package require psfgen

topology martini-protein.top
readpsf martininodisu.psf
coordpdb martininodisu.pdb
patch DISU Prot:15 Prot:278
writepsf martiniwdisu.psf
writepdb martiniwdisu.pdb

Assuming your segnames *are* actually Prot, this will add a single disulfide between residues 15 and 278.

-Josh

On 01/29/2018 02:35 AM, Shahee Islam wrote:
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<mailto: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<mailto: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