Hi,
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.
Pradipta
Received on Mon Aug 06 2001 - 16:45:00 PDT
