AMBER Archive (2009)

Subject: [AMBER] Half charge reported during NN ?

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Wed Jun 24 2009 - 11:33:54 CDT

Dear Amber users,

I found out that in sander minimisation output file which is produced as a
temporary result during normal mode analysis
there is always reported just half value of the real PRMTOP charge. Below
is one example.

In the output file from the minimisation of the first frame of my complex
"sanmin_com.1.out" is writen:

"Sum of charges from parm topology file = 235.00000048" although the real
charge written in PRMTOP file is +470.

The fact that the real PRMTOP charge is +470 is confirmed by this record
"Sum of charges from parm topology file = 0.00000097"
 from the output file obtained during the simulation in explicit water with
counterions with total charge -470.

So during the minimisation for the entropy calculation, charge is
probably automatically scaled down by coeficient 0.5 regarding to
setting of dielectric constant or something like that ?

Below is input file which is automatically created during NN analysis for
the system minimisation.

I saw above phenomenon also in another my systems so I really would like
to know the reason.

Thanks to anybody in advance for the relevant info !

   Best regards,

       Marek

////////sanmin_com.in////////

File generated by mm_pbsa.pl
  &cntrl
   ntxo = 1,
   ntf = 1, ntb = 0,
   dielc = 4,
   cut = 99.0, nsnb = 99999,
   scnb = 2.0, scee = 1.2,
   imin = 1, maxcyc = 100000,
   ncyc = 0, drms = 0.1
  &end
  &ewald
   eedmeth= 5,
  &end 

-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/

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