thansk!!!
I’ll try to use packmol, I think that for future versions of amber it woudl be a good idea to have the ability to produce solvent mixtures, it is very important for drug design and delivery.
Best,
fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 12 Nov 2015, at 8:39 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Thu, Nov 12, 2015, Fabian gmail wrote:
>>
>> I would like to create different solvent boxes and then run MD with
>> them, is there any protocol that describes in detail how to do it
>> properly?
>
> Amber doesn't really have tools for this. Try packmol to get the starting
> coordinates. Then run MD as you would for a pure solvent.
>
> ....dac
>
>
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Received on Sun Nov 15 2015 - 02:00:03 PST
