Re: Generate psf file in x-plor format

From: Nehad Elsalamouny (
Date: Thu Nov 17 2016 - 16:59:53 CST

Hi Josh,

The psf file is not truncated. I have just sent part of it as I couldn’t send it all (file is too big). I reran the script and still getting that same error: PSF file is in CHARMM format; XPLOR format required.

And in VMD TkConsole I get:

Info) generating solute plus one replica of water...
psfgen) reading structure from psf file xxxx.psf
psfgen) error reading atoms from psf file

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.



On 18 Nov 2016, at 7:56 AM, Vermaas, Joshua <<>> wrote:

Hi Nehad,

Take a look at the end of the psf file you sent. Its truncated midway through line 344. Your script to generate the psf looks solid, so I don't know how this happened. The truncation would be why solvate won't work on it. Did the psfgen script give you any errors? This is definitely weird, but might go away if you just rerun the generation script.

On 11/17/2016 01:47 PM, Nehad Elsalamouny wrote:
  Hi Josh,

  Thanks for your email. I got the rtf file from, downloaded toppar_c36_jul16.tgz<> and used the parm14sb_all.rtf file in non-charmm folder.
  Atomtypes are alphanumeric. Part of the psf file is attached. I don't know what is the problem!

  Kind regards,


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