Hi Ross,
I am working on MM PBSA..
As per the tutorial I am minimizing,heating & equilibrating the protein -ligand complex...
I used a step size of 0.001 ps for heating....
will it be ok for me to use a step size of 0.002 ps for equilibration and production MD coz running with 0.001ps is taking a lot of time...
I have applied SHAKE
Thanks
________________________________
From: Ross Walker <ross.rosswalker.co.uk>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 20 April, 2009 2:53:38 AM
Subject: RE: [AMBER] Atom type error
Hi Vikas,
> Now after loading the protein i wanted to solvate it, so i found out
> the charge in xleap using 'charge ' command..it comes out to be :
>
> 'total perturbed charge = 9.000100
> 'total unperturbed charge = 9.000100'
>
> i added 9 Cl- bt the charge still remains 0.000100...
> what should i do now...
This is an acceptable amount since most of the charges are only defined to 4
decimal places anyway. Sander / PMEMD will take care of this residual charge
when it runs.
All the best
Ross
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Received on Wed May 20 2009 - 11:56:35 PDT
