AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: Vikas Sharma (
Date: Tue Apr 21 2009 - 01:55:24 CDT

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

From: Ross Walker <>
To: AMBER Mailing List <>
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 ' 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

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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