Re: [AMBER] issues with pmemd

From: Ganesh Kamath <>
Date: Tue, 30 Mar 2010 15:14:54 -0400

 Thanks for the message. I was unsuccessful in using solvatebox. The protein
which is a fibrin has a y dimension of
around 250 A. It is made of 411 amino acids. The other dimensions are around
62 A each. I used around 30000 atoms with packmol program and saw that the
protein was completely immersed.
Is there a way I could still make use of solvate box. Even if i did I would
be having around 2 million atoms. I could resort to
implicit solvent or work with a few explicit solvents.

However I a compiled version of sander on my desktop and it was performing
the minimization "okay" but slow. I would
very much like to solvate this system. Could I get around with a few water
molecules (explicit).

Any suggestions please.

thanks for all the help.


On Tue, Mar 30, 2010 at 2:23 PM, case <> wrote:

> On Tue, Mar 30, 2010, Ganesh Kamath wrote:
> >
> > I have a system size of 303.4454000 303.3504000 303.3644000 box size and
> it
> > has 141000 atoms with water.
> Something is badly wrong here. Your unit cell volume is way too big for a
> system of 141,000 atoms. Roughly, that many atoms would occupy something
> like 1.5 x 10^6 A^3, but your unit cell is 27 x 10^6 A^3. You will need to
> re-visit the way you prepared the system.
> ....dac
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Received on Tue Mar 30 2010 - 12:30:03 PDT
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