VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Oct 26 2004 - 10:32:26 CDT

Psfgen only reads charmm *topology* files. It writes (and reads) x-plor
format *structure* (.psf) files using the charmm conventions for multiple
dihedrals (so they aren't the same as one written by x-plor, but it's
x-plor format because it has atom type names rather than numbers).

I don't know of any topology conversion tools other than "vi".

-Jim

On Tue, 26 Oct 2004, Charles McCallum wrote:

> Yes, psfgen takes xplor. I think that is the default. You can read in the
> xplor format and write out xplor or charmm format.
>
> HTH.
>
> Mike
> On Oct 26, 2004, at 06:17, Marc Q. Ma wrote:
>
>> Thanks, Charles. However, this link does not address my question. My
>> question is: Can psfgen take xplor topology files and generate psf files
>> for MD simulations? If psfgen does not take xplor topology file, is there
>> any tool to convert xplor topology to charmm topology?
>>
>> Marc
>> On Oct 25, 2004, at 11:33 PM, Charles McCallum wrote:
>>
>>> This is a FAQ (I know, I've sure asked it before!). Brian Bennon answered
>>> it it here:
>>>
>>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2190.html
>>>
>>>
>>> On Oct 25, 2004, at 13:08, Marc Q. Ma wrote:
>>>
>>>> Dear friends,
>>>>
>>>> Does anyone know how to convert xplor topology file to charmm topology
>>>> file? I am having troubles using psfgen because I need a charmm topology
>>>> file for describing my ligands, but I only have the xplor format
>>>> topology.
>>>>
>>>> Thanks,
>>>>
>>>> Marc
>>>> ----------------------------------------------------------------------
>>>> Marc Q. Ma, Ph.D. | Tel: 973-642-4497
>>>> Department of Computer Science | Fax: 973-596-5777
>>>> New Jersey Institute of Technology | Email: qma_at_oak.njit.edu
>>>> University Heights, Newark, NJ 07102 | URL: http://cs.njit.edu/~qma
>>>> ----------------------------------------------------------------------
>>>>
>>>>
>>> --
>>> C. Michael McCallum
>>> http://chem.cop.uop.edu/cmmccallum.html
>>> Associate Professor
>>> Department of Chemistry, UOP
>>> mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209)
>>> 946-2607 fax
>>>
>> Marc
>> ----------------------------------------------------------------------
>> Marc Q. Ma, Ph.D. | Tel: 973-642-4497
>> Department of Computer Science | Fax: 973-596-5777
>> New Jersey Institute of Technology | Email: qma_at_oak.njit.edu
>> University Heights, Newark, NJ 07102 | URL: http://cs.njit.edu/~qma
>> ----------------------------------------------------------------------
>>
>>
> --
> C. Michael McCallum
> http://chem.cop.uop.edu/cmmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209)
> 946-2607 fax
>