[Chimera-users] Question

Damjanovic Marko damjanovic at uni-heidelberg.de
Tue Jul 7 03:59:03 PDT 2015


Dear Dr. Meng,

thank you very much for the detailed email with the valuable advice. I 
will give AutoPack a try.

Best wishes,
Marko

Am 06.07.2015 um 22:47 schrieb Elaine Meng:
> Hello Damjanovic Marko,
> I don’t think Chimera can effectively address this problem.  Although there is a Solvate tool,
>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/solvate/solvate.html>
>
> ... it is basically an interface to Ambertools LEaP solvate commands.  From looking at the Ambertools “solvateShell”  description, I doubt it uses the approach you describe.  The Ambertools manual is available here (I’m looking at p. 222 of the 2015 manual):
> <http://ambermd.org/doc12/>
>
> One idea is to take a look at AutoPACK:
> <http://www.autopack.org/>
>
> 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 Jul 2, 2015, at 12:05 AM, Damjanovic Marko <damjanovic at uni-heidelberg.de> wrote:
>>
>> To whom it may concern,
>>
>> I am trying to solve a problem that is more of mathematical nature, and I would be very grateful if I could get any advice or pointers on how it may be possible to do this (in Chimera or some other program I am not aware of).
>>
>> I have a molecule that is more or less of cylindrical shape (quite simple shape). I would need a way to surround this molecule with a certain number of layers of solvent molecules that fit around the surface of a cylinder (preferably 1 layer and then going up gradually). The solvent molecules should be packed around the central molecule efficiently (closest packing). An alternative way to approach this would be to take a sphere made out of solvent molecules, put in the centre of the sphere the one cylindrical molecule what is of interest, and let the big sphere accommodate the new molecule. Also, for the sake of simplicity, the solvent molecules can be approximated as small spheres as well (their exact shape is not that relevant).
>>
>> When this is done, all I would need is to get this file in a format like cif, mol or gjf. I underline here that I am looking for a relatively crude model.
>>
>> Could anyone please advise me on how to do something like this?
>>
>> Thanks in advance and best wishes,
>> Damjanovic Marko

-- 
M.Sc. Dipl.-Chem. Damjanovic Marko
Anorganisch-Chemisches Institut
Universität Heidelberg
Im Neuenheimer Feld 270
D-69120 Heidelberg

Tel: +49(0)6221 54 6204/6205
Fax: +49(0)6221 54 161 6247
e-mail: damjanovic at uni-heidelberg.de



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