AMBER Archive (2004)

Subject: RE: AMBER: charge problem in minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 08 2004 - 12:40:56 CDT

Dear Yen,
 
Could you please post your prmtop file so that I can take a look at it and
ensure it has the correct charges. The charge reported in the output file
should match the prmtop file. So either there is a problem with sander OR a
problem with the prmtop file, and thus possibly with Leap.
 
Also, can you let me know what type of system you are running this on. Are
you running serial or parallel? And do all the test cases in
$AMBERHOME/test/ pass? If not, are the failures just minor rounding errors
or major differences?
 
All the best
Ross
 
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
yen li
Sent: 06 July 2004 23:33
To: amber_at_scripps.edu
Subject: AMBER: charge problem in minimization

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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