VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sun Aug 30 2020 - 06:39:36 CDT

Try the selection “segname AP1 DP1”.

Best,
JC

> On Aug 30, 2020, at 3:20 AM, Adupa Vasista <adupavasista_at_gmail.com> wrote:
>
> Thank you for the reply, I visualized using VMD, Here are the steps I followed to confirm a bond absence,
>
> 1) loaded the psf and pdb
> 2) I made the selections "Segname AP1" and "Segname DP1" and tried visualizing the bond.
>
> Surprisingly still I don't see a bond between index's 51829 and 4839. Sorry if I am missing anything simple or my understanding of patches is wrong.
>
> Thank you.
>
> On Sun, Aug 30, 2020 at 9:52 AM Peter Freddolino <petefred_at_umich.edu <mailto:petefred_at_umich.edu>> wrote:
> How did you try visualizing your file? The bond is present in the psf -- see here in the BONDS section:
>
> 51826 51828 51826 51827 51826 51819 51829 4839
>
> So the last entry in that row is a bond between the ND2 atom of N331 to the C1 atom of your BGLN4 residue.
> Best,
> Peter
>
> On Sat, Aug 29, 2020 at 6:18 AM Adupa Vasista <adupavasista_at_gmail.com <mailto:adupavasista_at_gmail.com>> wrote:
>
> Dear VMD Users,
> I am generating PSF using AutoPSF plugin in VMD version 1.9.4a38, My molecule contains a protein and a sugar. AutoPSF recognizes the required patches, So I generated the PSF and the process went smoothly. But when I visualize it by loading into VMD, I do not see any bond between the sugar and protein. Am I missing anything?
>
> The only change I made in the topology file(top_all36_carb.rtf) is changing the residue names from BGLCNA and BGLCN0 to BGLN.
>
> I also tried to apply the patch manually taking the patching information from AutoPSF, but results in an error saying
> patch NGLB AP1:331 DG1:4
>
> psfgen) applying patch NGLB to 2 residue(s)
> psfgen) no segment AP1
>
> I have checked for that segname, It is present, but still the error exists.
>
> Help me in this regard.
>
> Here, I attach the pdb of the molecule and the psf generated by AutoPSF.
>
> I am Sorry, if the mail came twice.
>
> Thank you.
>
>
>
>  6vxx_model_01_chainD_autopsf.psf <https://drive.google.com/file/d/1kNodhx6aPj3wKZErGXSN-TY-koRx6xHr/view?usp=drive_web>
>
>  6vxx_model_01_chainD.pdb <https://drive.google.com/file/d/11Y6ZPsulCqT6T3zlViAle9niRlBAskNM/view?usp=drive_web>
>
>
> --
> A.Vasista
> M.Tech,Department Of Chemical Engineering,
> IIT Guwahati.