Leap and parm/pert!

From: PRADIPTA Bandyopadhyay <pradipta_at_cgl.ucsf.edu>
Date: Mon 6 Aug 2001 16:45:00 -0700 (PDT)


   I have a problem with the total charge of my system
(protein+ligand) when I save the topology file as saveamberparmpert.

 For exactly the same unit when I save as saveamberparm - the total chrage
of the system is -0.006 ( which is correct - since I have some non-standard
 residues and some of my charges are not AMBER charges - so it is
 not exactly integral though very close). However, if I save the same
 unit as saveamberparmpert - the total charge becomes -0.1403 for the
 initial state and -0.1129 for the final state ( for the final state
 the actual charge is -0.007).

 I don't how I am getting this bizarre result?

 I am doing the following things in Leap:

 1) Loading my 4 non-standard residues.
 2) Loading new parameter file.

 3) using the BOND command to connect some of the new residues.

 4) setBox to enforce periodicity ( I am getting the PDB file from an
    initial MD run -so it has Na+ counterions and waters).

 4) saveamberparm or saveamberparmpert.

Any suggestion would be appreciated.

Received on Mon Aug 06 2001 - 16:45:00 PDT
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