AMBER Archive (2007)

Subject: Re: AMBER: ADDIONS do not neutralize to ZERO

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Mon Jan 29 2007 - 15:30:20 CST

It sounds like you have many hundreds of DMP residues and these
non-integral charges are adding up badly.

If this is the case, you may want to take time to use the RED perl
scripts with multiple orientations of DMP - and possibly multiple
conformations:

http://www.u-picardie.fr/labo/lbpd/RED/

This may give you greater confidence in your DMP charges. Then, if you
still must hand-adjust some atoms by .000005 or so, I believe that you
can do this without much guilt.

Chris

Adding .00005 charge units to 4 DMP atoms to solve this is

Regarding my charge of 0.970410 in the system, I checked and my system
> without ligand, and you are right>>
>
> Total unperturbed charge: 13.9705
> Total perturbed charge: 13.9705
>
> So, my system (protein-lipid-water) essentially has a + 13.9705 charge. Now,
> I also checked my lipid (DMP) unit for charge, and although it should be
> neutral, It has a residual charge of::
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu