From: Peter Freddolino (
Date: Fri Jul 05 2019 - 08:02:29 CDT

Changing the names should not change the structure... the most likely cause
(although I cannot tell for sure unless you post the relevant files) is
that you did not keep the columns of the pdb file properly aligned after
changing the names. The PDB format is fixed width, so if you add a few
characters to the name, you have to delete spaces to keep the coordinate
columns in their proper places.

On Fri, Jul 5, 2019 at 12:41 AM Adupa Vasista <>

> and also if I change the atom names as per the RTF file, then the entire
> structure is changing.
> I am changing the Atom name in the 3rd column of the PDB.
> Thank you
> On Fri, Jul 5, 2019 at 3:38 AM Peter Freddolino <>
> wrote:
>> 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...
>> Best,
>> Peter
>> 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)
> --
> *A.VasistaM.Tech,Department Of Chemical Engineering,*
> *IIT Guwahati.*