From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Sun Aug 30 2020 - 02:20:32 CDT

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> 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>
> 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.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*