Hi,
You can also try the packmol-memgen wrapper. In the new AmberTools19
release (availabe sometime next month I guess), I support some more
functionalities for non-membrane packing, and there you can include solutes
at whatever concentration you want. I am interested in feedback about this,
so let me know if there is something jn particular you need. I guess I
could include some solvents aside from water...
Cheers,
El mar., 26 mar. 2019 a las 17:55, Debarati DasGupta (<
debarati_dasgupta.hotmail.com>) escribió:
> Hi Matt,
> yes it is straightforward to prepare mixed solvent boxes in amber as long
> as you know the concentrations you want and the prepi and frcmod parameters
> for those solvents.
> You can also use Packmol (http://m3g.iqm.unicamp.br/packmol/home.shtml)
> to define a fixed number of water + co solvent molecules you need for
> solvating your polymer of interest.
>
> Thanks
> Debarati
>
> ________________________________
> From: Defrese, Matthew <matthew.defrese.uky.edu>
> Sent: Tuesday, March 26, 2019 8:57 PM
> To: amber.ambermd.org
> Subject: [AMBER] Solvate with methanol and acetone using free energy
> methods?
>
> Hello,
>
>
> We are looking to model a system consisting of ligand binding to a
> synthetic polymer in varying solvent conditions such as water, acetone,
> methanol and their mixtures. Is there a straightforward way of solvating a
> box with these types of solvents in AMBER? We have seen that we can solvate
> with pure methanol, though not for acetone or their mixtures with water.
>
>
> Is setting up and running free energy calculations in AMBER similar or
> equivalent to NAMD in terms of user friendliness?
>
> Thank you for any assistance,
>
>
> - Matt Defrese
>
> Graduate Student, Marsac Lab, Dept. of Pharmaceutical Sciences
>
> College of Pharmacy, University of Kentucky
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sat Mar 30 2019 - 15:00:04 PDT
