From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sat Feb 15 2014 - 11:30:42 CST
Even if it were "parameterized well" (for which the tool you're using
doesn't seem appropriate), you still have to worry about it being
physically compatible with the force field you're using for your
biomolecule. I could suggest better tools, but my suggestion would depend
on the choice of biomolecular force field, so you'd have to answer the
questions in my previous post first. As a general rule, if we take the
time to ask questions, we do so for a reason...
On 02/15/2014 05:34 AM, Anna Borlsky wrote:
> Dear Kenno and other members of namd mailing list,
>
> Is it coumarin. I am planning at the begining only to simulate coumarin
> alone to see if it was well parameterized. The topology and the parameter
> files were generated by xplo2d and are in xplor format. Please find
> attached the files.
>
> Kind regards,
> Anna
>
>
> 2014-02-14 1:48 GMT+00:00 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu
> <mailto:kvanomme_at_rx.umaryland.edu>>:
>
> Please reply to the list, not to people's personal e-mail.
>
> I'll need some more details to be of any help. Is this a lipid or a
> cofactor or a drug-like molecule? Are you planning to simulate its
> interaction with a biomolecule (such as a protein or nucleic acid)? If
> yes, what force field are you planning to use for the biomolecule?
>
> Best regards,
>
> Kenno.
>
> On 02/13/2014 07:12 PM, Anna Borlsky wrote:
>
> Dear Kenno,
>
> My problem is that I generated the topology and the parameter file
> using
> xplo-2d and the multiplicities are zero on the parameter file what
> makes
> no sense so I should change it. My problem is that I do not know which
> values of multiplicities give. All dihedrals with multiplicity 2 is
> probably not ok. I have sp2 carbons on my molecule.
> I have also doubts in attribute multiplicities when I have two
> dihedrals
> that are the same but only differ on the value of the angle (one
> with 180º
> and the other one with 0º).
>
> Best regards,
> Anna
>
>
>
>
> 2014-02-13 23:53 GMT+00:00 Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>
> <mailto:kvanomme_at_rx.umaryland.__edu
> <mailto:kvanomme_at_rx.umaryland.edu>>>:
>
>
> Additionally, users should leave the force fields alone
> unless they're
> really really sure of what they're doing.
>
>
> On 02/13/2014 03:23 PM, Norman Geist wrote:
>
> Additionally, this has nothing to with namd but with
> forcefield
> definitions.
>
> Norman Geist.
>
>
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>
> <mailto:owner-namd-l_at_ks.uiuc.__edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>>
> [mailto:owner-namd-l_at_ks.uiuc.
> <mailto:owner-namd-l_at_ks.uiuc.>____edu
>
> <mailto:owner-namd-l_at_ks.uiuc.__edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>>] Im
> Auftrag von Jeffrey Potoff
> Gesendet: Donnerstag, 13. Februar 2014 18:34
> An: Anna Borlsky
> Cc: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> <mailto:namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
>
> Betreff: Re: namd-l: Dihedrals multiplicity!
>
> On 02/13/2014 12:27 PM, Anna Borlsky wrote:
>
> Dear Jeffrey,
>
> Thank you very much for the link, but I did not
> found in
> it an answer
> to my question.
> What I see is that when I changed the
> multiplicity of the
> dihedrals
>
> in
>
> namd the molecule twisted. But I do not know
> which are the
> right
> multiplicities to use and what does they mean in the
> simulation.
>
> Best regards,
> Vanessa
>
> Try this one:
>
> http://www.ks.uiuc.edu/____Training/Tutorials/science/____forcefield-
> <http://www.ks.uiuc.edu/__Training/Tutorials/science/__forcefield->
>
> <http://www.ks.uiuc.edu/__Training/Tutorials/science/__forcefield-
> <http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield->>
> tutorial/forcefield-html/____node6.html
>
>
> Specifically, you should read the section entitled "A
> Closer
> Look at
> Dihedral Parameters"
>
> --
>
> ==============================____============================__==__==========
> Jeffrey J. Potoff jpotoff_at_wayne.edu
> <mailto:jpotoff_at_wayne.edu> <mailto:jpotoff_at_wayne.edu
> <mailto:jpotoff_at_wayne.edu>>
>
> Associate Professor and Director of Early Engineering
> Programs
> Department of Chemical Engineering and Materials Science
> Wayne State University 5050 Anthony Wayne Dr
> Detroit, MI 48202
> http://potoff1.eng.wayne.edu
>
> ==============================____============================__==__==========
>
>
>
>
>
>
>
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