Dear Amber Users:
I am using the QM/MM interace, via the &qmmm namelist, to do a PM3 calculation on a dimer that contains one cadmium and one selenium.
1. In tleap, the molecule is constructed as one unit containing one residue, from the pdb file:
cdse=loadpdb cdse.pdb
2a. To make tleap write the prmtop and inpcrd files, I specified the type using the commands:
set cdse.0.1 type Se
set cdse.0.2 type Cd
2b. I typed "desc cdse.0.1", and I get:
ATOM
Name: Se
Type: Se
Charge: -0.6000
Polarization: 0.0000
Element: Se
So tleap recognizes the elements
2c. I loaded the parameters file "cdse.frcmod". It contains dummy values, but I don't think this matters.
loadamberparams cdse.frcmod
The exact commands I typed are contained in the attachment "leap.in". The topology and coordinates files are in "cdse.prmtop" and "cdse.inpcrd".
4. I run a minimization with the options:
&cntrl
imin=1, maxcyc=500, ncyc=200, cut=12.0, ntb=0, ntc=1, ntf=1, ifqnt=1
/
&qmmm
qmmask=':1', qmcharge=0, qm_theory='PM3',
/
5. QM/MM assigns 'C' instead of 'Cd' and 'S' instead of 'Se':
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 S 1.4800 2.4250 1.5280
QMMM: 2 2 C -1.1160 2.0420 1.2060
I can't find the documentation to guide me. I encounter the same issue when the molecule contains both QM and MM atoms.
Chris Liu
Received on Wed May 20 2009 - 14:15:15 PDT
