VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Tue Oct 26 2004 - 11:25:56 CDT

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
----------------------------------------------------------------------