AMBER Archive (2005)

Subject: Re: AMBER: SollvateBox with ethanol

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Fri Apr 15 2005 - 12:50:20 CDT

Hi,

Assuming the methanol in amber is called METHANOL, then you can create a
methanol box by

mbox = copy METHANOL
solvatebox mbox METHANOL 10
setbox mbox vdw
saveamberparm mbox mbox.top mbox.crd

Then you need to equilibrate this methanol box with some MD steps, and
build a unit from the relaxed box. Or you can apply the above recipe to
your B-DNA.

Guanglei

Huaer XC wrote:
> Hi, all:
> I have a question with the LEaP. I want to simulate a B-DNA helix in
> ethanol. But I don't know how to make a solvateBox of ethanol in LEaP,
> which seems not in AMBER's manual(I can find water, methanol anyway).
> Can anyone in group give me some advices? I am very new to this field,
> and hope to get some points from learning in this group. Thanks in
> advance.
> Huaer
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