Re: vmd-l: psfgen and xplor topology

From: Charles McCallum (mmccallum_at_pacific.edu)
Date: Tue Oct 26 2004 - 11:36:37 CDT

Seems I was wrong -- I apologize profusely! I guess every time we put
a new system into NAMD (from charmm) we go through this,
which is why I thought psfgen must take xplor (since we successfully
get things into NAMD). I agree with you Marc, that it would
be nice if psfgen could read xplor. I think the reasoning is that most
people will be coming from charmm into NAMD, but it should not
be exclusive. There is certainly enough of that around! I think amber
can read/write xplor but not charmm, for example.

Cheers,

Mike
On Oct 26, 2004, at 09:25, 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
> ----------------------------------------------------------------------
>
>

--
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

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