[Chimera-users] Regarding organic molecule minimization

Satheesh G gschemie at gmail.com
Mon Sep 29 20:07:10 PDT 2014


Thank you all for your suggestions.

On Mon, Sep 29, 2014 at 10:57 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Satheesh,
>         The geometry of the minimized molecule will depend on the GAFF
> atom types assigned to the nitrogens by Antechamber.  In Chimera, use
> Actions->Label->other… to show the "gaffType" labels on the atoms.  Make
> sure the nitrogens have the n2 GAFF type (sp2 N with 2 substituents) rather
> than n1 (sp1 N).  If they don't have the right types, select the two N
> atoms and use this command to change the type:
>
> setattr a gaffType n2 sel
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
> On Sep 29, 2014, at 10:06 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> > Dear Satheesh,
> > Amber's Antechamber module (included with Chimera) is used to assign
> parameters to nonstandard residues, as mentioned here:
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#nonstandard
> >
> >
> > ("standard" includes include water, standard amino acids, standard
> nucleic acids, and a few common variants and capping groups, whereas
> "nonstandard" is everything else)
> >
> > It may be a limitation of the Antechamber program.  You could look at
> the Antechamber reference (given in the link above, also here <
> http://www.ncbi.nlm.nih.gov/pubmed/16458552>) to see if the authors
> included azo groups in their development.  Scanning Figure 1 in that paper,
> I see double- and triple-bonded nitrogen but not your specific case.   Even
> if the Antechamber parameters are meant to handle the azo group, it may be
> that the input bond lengths and angles are bad and prevent the group from
> being recognized correctly, in other words, maybe with better input bond
> lengths and angles it would minimize correctly.  I don't know which of
> these might be the case.  You could try asking about this on the AMBER
> mailing list instead.
> >
> > My only other idea is to obtain a structure that is already minimized or
> rule-built to a good geometry instead of trying to minimize it in Chimera.
> For example, if you know the Pubmed CID or SMILES string for this compound,
> you could try to get the already-minimized structure opened in Chimera by
> PubMed or SMILES fetch.  In Chimera, you could try that in Build Structure
> (in menu under Tools… Structure Editing), "Start Structure" tab, options
> "SMILES string" or "PubChem CID".  See description here:
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
> >
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Sep 27, 2014, at 6:15 AM, Satheesh G <gschemie at gmail.com> wrote:
> >
> >> Dear Sir,
> >>
> >> The azo compounds (organic molecule) minimization using Chimera
> software giving linear form (R-N=N-R  to R-N=N-R (180 degrees bong angle
> between  R-N=N instead  R-N=N- 120 degrees). Which is not true. I have used
> the gasteiger and  amber ff12sb force field. Please suggest me to solve
> this problem.
> >>
> >> Thanking you.
> >>
> >> Satheesh.
> >>
> >
> >
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>
>
>
>
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