From: Chitrak Gupta (
Date: Fri Apr 08 2016 - 16:40:46 CDT

Hi Srijita,

You have to make sure that the molecules you have in your system are
defined in the topology file(s) that you are including. I think urea is
defined in either the top_all36_cgenff.rtf file. I am not sure about the
choline-o-sulfate, but you could look through the other topology files.

Hope this helps,

On Fri, Apr 8, 2016 at 2:49 PM, Srijita Paul <> wrote:

> Thanks for your kind reply.I want to put urea and choline-o-sulfate with
> the protein.I have included the topology file top_all36_prot.rtf. Is it not
> enough for this case? Should i include individual topology files for urea
> and choline-o-sulfate?
> On Fri, Apr 8, 2016 at 8:31 PM, Chitrak Gupta <> wrote:
>> Hi Srijita,
>> What other molecule (apart from protein) did you have in your system? Did
>> you include topology files for those molecules? If not, PSFGEN will not be
>> able to find connectivity information for those molecules.
>> Best,
>> Chitrak.
>> On Fri, Apr 8, 2016 at 9:00 AM, Srijita Paul <>
>> wrote:
>>> Hi.
>>> Is it possible to create a psf file using a pdb file created from
>>> packmol? actually i want to generate a system combining to different
>>> molecules in packmol.but when i am trying to generate the psf file using
>>> psfgen the psf file only giving the information about the protein and
>>> others molecules are missing in the psf file.plz suggest either there is
>>> any other option to pack different molecules in one system without using
>>> packmol.
>>> thank you

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