Ok, thank you David.
On Thursday, September 10, 2015 8:32 PM, David A Case <david.case.rutgers.edu> wrote:
On Thu, Sep 10, 2015, mohammad r wrote:
> I am new user toamber. I want to set a cubic box around my lipid-peptide
> system, Iknow that the “setBox” command do this, but I don't know
> how Ican specify the dimensions of the box and how to specify its
> center(indeed I want the dimensions to be constant). It isn't mentioned
> inthe tutorial. How can I specify these parameters?After this I want to
> Dissolve it in water andI don't know which command does it in tleap.
"solvatebox" is the command in LEaP to both set up the box and add solvent.
(If you just want to set up the box, use the "set <unit> box...." command.
However, LEaP is not well set up to allow you to create a solvent box with
specific box dimensions. You might want to look at the packmol program for
this sort of functionality. (Or, consider whether you really need such
features....there is a reason they are not present in Amber: Amber users don't
see a need for them.)
....dac
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Received on Thu Sep 10 2015 - 11:00:03 PDT
