VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Thu Jul 04 2019 - 14:54:25 CDT

I have been facing this problem since last week,
1) I have taken a Ligand which is SDF format and converted in PDB using
openbabel.
2) uploaded to LigParGen/CGenFF to get the topology files. I got the
topology files.

3) I opened the PDB in VMD and Using the RTF file generated by
LigParGen/CGenFF in AutoPSF; I got psf and PDB.

4) when I look at the PDB generated by Autopsf all the coordinates are
alike, and I am getting a single atom when I load it in VMD.

Here I attach all the related files; please look into it.

Attached files 1) 1.sdf from the internet
                         2) 1.pdb using OpenBabel
                         3)1_autopsf.pdb and psf which are generated by
AutoPSF
                         4) RTF file generated by LigParGen (CHARMM force
field)


  • application/x-aportisdoc attachment: 1.pdb
  • application/octet-stream attachment: 1.sdf