AMBER Archive (2005)

Subject: Re: AMBER: Controlling number of water residues...

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue Mar 01 2005 - 09:49:57 CST

Hi,

I'm not sure if this is the best to solvate system with pre-defined
number of water molecules. But you could try to solvatebox with certain
buffer size which gives you somewhat more solvent molecules. Then you
can write a shell script to create a leaprc file to remove those extra
solvent molecules. Perhaps this may give you better luck with relaxing
the system.

Guanglei

Pavan G wrote:
> Hi
>
> I am trying to build a system of a protein surrounded by a pre-defined
> number of water residues. However, when I solvated the protein using
> the solvatebox command the number of water residues added far exceeded
> the desired number.
>
> I have tried to perform MD on a system of a protein surrounded by 10
> boxes each containing 210 water residues ( which is obtained by
> solvating a water molecule) with the idea that periodic boundary
> conditions will take care of the obvious problem in which water
> residues fly off. The 10 boxes were placed randomly. However, the
> system was fine till minimization was over but on running MD (sander),
> it gave no output, both the .out and .mdcrd files were empty. I
> suspect that large empty (vaccum) spaces around the boxes might have
> led to instabilities.
>
> Please let me know what the problem is and suggest an appropriate solution.
>
> Pavan Ghatty
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu