VMD-L Mailing List

From: Akash Mondal (akmondal1013_at_gmail.com)
Date: Sat Sep 03 2022 - 01:37:41 CDT

Dear Community,
I made a small mistake, I have modified the patch line as follows
patch SUCR SUC:1 SUC:2
Now it works.
Thank you

On Sat, Sep 3, 2022 at 11:44 AM Akash Mondal <akmondal1013_at_gmail.com> wrote:

> Dear Community,
> I'm trying to make a sucrose molecule using psfgen.
>
> I used the following pgn file
> "package require psfgen
> topology top_all36_carb.rtf
>
> alias residue GLC AGLC
> alias residue FRU BFRU
>
> segment SUC {
> pdb sucrose.seg.pdb
> }
> patch SUCR SUC:1
> coordpdb sucrose.seg.pdb SUC
> guesscoord
>
> writepdb sucrose.fin.pdb
> writepsf sucrose.fin.psf"
>
> then called using the following command
> vmd -dispdev text -e file.pgn
>
> I got the following error:
>
> psfgen) aliasing residue GLC to AGLC
> psfgen) aliasing residue FRU to BFRU
> psfgen) building segment SUC
> psfgen) reading residues from pdb file sucrose.seg.pdb
> psfgen) extracted 1 residues from pdb file
> Info: generating structure...
> segment complete.
> psfgen) applying patch SUCR to 1 residue(s)
> ERROR: failed to apply patch
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> Can anybody suggest to me what mistake I'm making?
>
> For better understanding, I have attached the sucrose pdb file. Plz help
> me.
>
> Thank you
>