[Chimera-users] Regarding organic molecule minimization

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 29 10:27:40 PDT 2014

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 Pettersen
                        UCSF Computer Graphics Lab

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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