From: Anna Borlsky (annanamd_at_gmail.com)
Date: Sat Feb 15 2014 - 11:51:16 CST
Dear Kenno,
I am sorry but I am new in modelling and namd so many concepts I do not
understand yet. As far as I know the topology and the parameter file
together create the force field and they were generated by program xplo2d.
Before submitting the pdb file to xplo2d I optimized the molecule with
MMFF94s force field. So probably it is the name of the bimolecular force
field, isn't it?
Kind regards,
Anna
2014-02-15 17:30 GMT+00:00 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>:
> 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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