VMD-L Mailing List

From: Akash Mondal (akmondal1013_at_gmail.com)
Date: Sat Sep 03 2022 - 01:14:51 CDT

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