Hi
I am trying to neutralize my protein complex by adding Na+ ions to it
addions COM Na+ 0
which seems to do the right thing
Calculating grid charges
charges: 242 sec
(No solvent overlap)
Placed Na+ in COM at (24.80, -2.21, 25.46).
(No solvent overlap)
when I want to same the prmtop and inpcrd it gives me the following error
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+
the libraries loaded are
Loading parameters: /amber10/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0
Loading library: /amber10/dat/leap/lib/all_amino10.lib
Loading library: /amber10/dat/leap/lib/all_aminoct10.lib
Loading library: /amber10/dat/leap/lib/all_aminont10.lib
Loading library: /amber10/dat/leap/lib/all_nucleic10.lib
Loading library: /amber10/dat/leap/lib/ions08.lib
Loading library: /amber10/dat/leap/lib/solvents.lib
so I thought that I should have loaded everything - if I try desc Na+ it
returns the following
UNIT name: Na+
Head atom: null
Tail atom: null
Contents:
R<Na+ 1>
which seem to be ok - any suggestions how to fix this ?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 25 2010 - 11:00:03 PDT
