Re: AW: Dihedrals multiplicity!

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sat Feb 15 2014 - 22:15:33 CST

In research, as in many other aspects of life, you often have to think a
few steps ahead. Suppose you somehow succeed to fix up the topology and
parameter file xplo2d gave you. Then you have *a* force field for your
molecule. This might enable you "at the begining only to simulate coumarin
alone", as you put it. But "at the beginning" implies there's a next step?
What's the next step? Typically it would be to simulate your molecule
together with a biomolecule. So you'll need a force field for your
biomolecule as well. But different force fields cannot be assumed to be
physically compatible. If you followed a CHARMM methodology for
parameterizing your small molecule and you choose the AMBER force field
for your biomolecule (or vice versa), any knowledgeable reviewer will
shoot down your work. If you followed a parameterization methodology that
is not associated with any biomolecular force field (for example by using
parameters from MMFF94), well then you can restart from scratch.

It's a bit worrisome that your mentor apparently didn't warn you about
these things.

For the specific case of coumarin, someone in out lab parameterized it a
few months ago. It's not officially released yet but I can give it to you.
However, it's a CHARMM parameter set, so it will only be of use to you if
you'll later use the CHARMM force field for your biomolecule. So you'll
first have to make certain you can do that. If not, there exist tools to
parameterize small molecules for other biomolecular force fields eg. AMBER.

By the way, you probably don't want to simulate your molecule "alone" in
vacuum, because most properties of interest are not measured in vacuum.
You'll typically need a water model. CHARMM is parameterized for the TIP3P
(explicit) water model, though it also has been used with some implicit
solvent models.

On 02/15/2014 12:51 PM, Anna Borlsky wrote:
> 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
> <mailto: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>
> <mailto: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>>
> <mailto:kvanomme_at_rx.umaryland.
> <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>>>
> [mailto:owner-namd-l_at_ks.uiuc
> <mailto:owner-namd-l_at_ks.uiuc>.
> <mailto:owner-namd-l_at_ks.uiuc
> <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>>
> <mailto: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->>
>
>
> <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>>
> <mailto: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
>
>
> ==============================______==========================__==__==__==========
>
>
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:29 CST