I, as many other people, truely really wish VMD finally can make that happen. I made the same problem with the ligand from HICUP...I was trying to hard to convert the topology myself and never made it (:-
>From: "Marc Q. Ma" <qma@oak.njit.edu>
>To: Jim Phillips <jim@ks.uiuc.edu>
>CC: Kentaro Sugino <ks23@njit.edu>, Charles McCallum <mmccallum@pacific.edu>, vmd-l@ks.uiuc.edu
>Subject: Re: vmd-l: psfgen and xplor topology
>Date: Tue, 26 Oct 2004 12:25:56 -0400
>
>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@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@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@oak.njit.edu
>University Heights, Newark, NJ 07102 | URL:
>http://cs.njit.edu/~qma
>----------------------------------------------------------------------
>
