[Chimera-users] Question

Repic Matej matej.repic at epfl.ch
Mon Jul 6 21:22:09 PDT 2015


You can also use Packmol to cylindrically pack the solvent(s) around the
solute. Multiple layers can also be assigned, it just takes some practice
to get the input file right.

http://www.ime.unicamp.br/~martinez/packmol/


------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne

------------------------------------------------------






On 7/6/15, 22:47, "chimera-users-bounces at cgl.ucsf.edu on behalf of Elaine
Meng" <chimera-users-bounces at cgl.ucsf.edu on behalf of meng at cgl.ucsf.edu>
wrote:

>Hello Damjanovic Marko,
>I don¹t 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 ³solvateShell²  description, I doubt it
>uses the approach you describe.  The Ambertools manual is available here
>(I¹m 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
>
>
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