Re: Problem generating pdb psf of ATP

From: Brian Radak (
Date: Mon May 14 2018 - 11:35:17 CDT

Can you explain what you mean by "wrong bond connectivity"? What was the
exact process by which you reached that conclusion?

The atom names in atp_namd.pdb (which I assume is your input to psfgen) do
not match those in the residue definition. This will result in a lot of
coordinate guessing, which is not always good in psfgen depending on the IC
table definition in the RTF.

On Mon, May 14, 2018 at 3:33 AM, Srijita Paul <> wrote:

> Hi,
> I have a pdbfile(atp_namd.pdb) of ATP which is attached here which
> contains ATP and Mg. I am trying to generate pdb and psf file of it using
> the topology files mentioned below-
> top_all36_cgenff.rtf
> top_all36_na.rtf
> toppar_all36_na_nad_ppi.str
> toppar_water_ions.str
> But after generating the pdb psf using psfgen I am getting a pdb which
> have some wrong bond connectivy (atp_new.pdb).
> What is the solution of the following problem?

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