AMBER Archive (2004)

Subject: AMBER: charge problem in minimization

From: yen li (chem_me2000_at_yahoo.com)
Date: Wed Jul 07 2004 - 01:33:09 CDT

Hi amber friends,

I have a problem in the minimization of a charged argenine dipeptide molecule (overall charge is +2 units). I am using AMBER7 and the distance dependent dielectric for the simulation. The input file is given as below

&cntrl

        imin=1,

        ntx=1,ntb=0,

        ntr=0,dielc=4,cut=300,

        maxcyc=1000, ncyc=500,

 &end

 &ewald

        use_pme=0,

        eedmeth=5,

 &end

 

The problem is that in the output file where it shows the ‘sum of charges from parm topology file’ is giving +1 unit (output file is attached). When I have tried the same for one more system containing only the C-terminal alanine peptide, the charge on the molecule is -1.0 unit, but in the output file the charge is -0.5 unit. When the same is done for the alanine dipeptide, where the overall charge is zero, the output file also reports the charge to be zero.

I want to know that what is the possible reason of the charge getting reduced to exactly half in the cases when there is a overall charge on the molecules, and is it affecting the electrostatics calculations and has it anything to do with the ewald option which is off in the present case.

Thanks.

                
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