AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Mon Apr 20 2009 - 05:46:34 CDT

Hi Ross..
Thanks a lot for the reply

________________________________
From: Ross Walker <ross_at_rosswalker.co.uk>
To: AMBER Mailing List <amber_at_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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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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