AMBER Archive (2002)

Subject: Re: charges

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 07 2002 - 20:35:07 CDT

On Tue, Aug 06, 2002, Cozmuta wrote:
>
> Leap is warning me that the unperturbed charge of the unit 7 is not
> zero meaning that my structure bears a charge of +7. However if I load the
> same file in another program (InsightII) and use the amber ff, the total
> charge on the structure is zero. I tried to look into the code
> ($AMBERHOME/src/leap/src/leap/unit.c) but I could not figure out how this
> charge was obtained and which residues have the charge that does not
> compensate. I would appreciate any useful hints that would help me
> understand this.
>

You can check the charges yourself by using the "edit" option in xleap
(select what you want, and choose "edit selected atoms"). You can also
to use the -pqr option in ambpdb to print out the charges. This should help
you figure out what you have.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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