VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Oct 26 2004 - 13:31:45 CDT

HIC-Up (http://xray.bmc.uu.se/hicup/) looks like a great tool, especially
combined with the PRODRG server and running XPLO2D manually when gets you
most of the way to an explicit hydrogen X-PLOR topology file.

There was a NAMD-L thread on this last month:

   http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1337.html

This is clearly a problem that needs to be solved. I've added it to
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdRequests for now,
but it's a broader, CHARMM forcefield-level problem.

-Jim

On Tue, 26 Oct 2004, Marc Q. Ma wrote:

> Thanks, Jim. This confirms with my experience.
>
> x-plor topology files are one of the outputs of HicUP which is very popular
> for generating topologies for novel molecules including ligands.
> Unfortunately, it does not output charmm format topology files.
>
> Are the NAMD/VMD group interested in providing a toolkit that translates
> xplor topology to charmm topology? With such a translator, NAMD and VMD will
> be more popular.
>
> Right now, we will stick with the quick-and-dirty hand editing using a text
> editor since my ligand structure is small.
>
> Marc
>
> On Oct 26, 2004, at 11:32 AM, Jim Phillips wrote:
>
>>
>>
>> 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
>>>
>>
>>
> 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
> ----------------------------------------------------------------------
>