VMD-L Mailing List

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Tue Oct 26 2004 - 09:50:08 CDT

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