Re: vmd-l: Getting the topology,PSF files

From: Peter Freddolino (
Date: Thu Jul 04 2019 - 17:09:41 CDT

Dear Adupa,
Did you try following the advice that was given in response to your prior
emails, of ensuring that the atom names in your .pdb file match those from
the ATOM entries in your .rtf file? If so, that is certainly not reflected
in the input pdb that you have posted...

On Thu, Jul 4, 2019 at 5:16 PM Adupa Vasista <> wrote:

> 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)

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