From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Apr 30 2009 - 11:22:01 CDT
Hi Matt,
You can find a CHARMM topology for benzene in the standard force field
distribution (link provided by Chris). The file you need is:
topar/stream/toppar_all22_prot_model.str
The residue is called BENZ.
Jerome
On Wed, Apr 29, 2009 at 8:29 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
> Matt
>
> It's actually not an issue of whether or not NAMD will treat it properly but
> whether or not the forcefield contains parameters for the molecule you wish
> to simulate. NAMD uses forcefield parameters, specified by the user, in
> order to perform simulations. There are several standard forcefields:
>
> For the CHARMM forcefield see
> http://mackerell.umaryland.edu/CHARMM_ff_params.html.
>
> For the AMBER forcefield see http://ambermd.org/dbase.html.
>
> NAMD is able to use both the CHARMM and AMBER forcefield, as well as that
> used in GROMACS, OPLS.
>
> To build a protein structure file of benzene, you would want to use the
> Molefacture plugin in VMD (http://www.ks.uiuc.edu/Research/vmd/) to build
> your benzene structure. If you wish to then simulate it you would use NAMD
> (http://www.ks.uiuc.edu/Research/namd/)
>
> To begin, I suggest looking at our tutorials which quickly teach you to use
> VMD and NAMD (http://www.ks.uiuc.edu/Training/Tutorials/). The beginning
> two initial tutorials for VMD and NAMD are available at:
>
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
>
>
> C.
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
>
> On Wed, Apr 29, 2009 at 7:04 PM, Matt Krems <mkrems_at_physics.ucsd.edu> wrote:
>>
>> Hello,
>>
>> I am trying to generate a protein structure file for benzene. It seems
>> pretty uncommon to look at structures this small in NAMD. Does anyone know
>> how to do this, and if so does NAMD actually treat such small molecules
>> accurately?
>>
>> Thanks,
>> Matt
>>
>
>
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