AMBER Archive (2009)

Subject: [AMBER] QM/MM assigns Cd to C, Se to S

From: C Liu (attobrain_at_rocketmail.com)
Date: Sat May 02 2009 - 21:09:27 CDT

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
   
   

       

remark goes here
MASS
Se 78.960 2.900 ATTN, need revision
Cd 112.411 2.900 ATTN, need revision

BOND
Se-Cd 10.000 2.70

ANGLE

DIHE

IMPROPER

NONBON
  Se 2.0000 0.2000 ATTN, need revision
  Cd 2.0000 0.2000 ATTN, need revision


     2
   1.4800000 2.4250000 1.5280000 -1.1160000 2.0420000 1.2060000


%VERSION VERSION_STAMP = V0001.000 DATE = 05/02/09 16:59:19
%FLAG TITLE
%FORMAT(20a4)
                                                                                
%FLAG POINTERS
%FORMAT(10I8)
       2 1 0 0 0 0 0 0 0 0
       2 1 0 0 0 0 0 0 2 0
       0 0 0 0 0 0 0 0 2 0
       0
%FLAG ATOM_NAME
%FORMAT(20a4)
Se Cd
%FLAG CHARGE
%FORMAT(5E16.8)
 -1.09333800E+01 1.09333800E+01
%FLAG MASS
%FORMAT(5E16.8)
  7.89600000E+01 1.12411000E+02
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
       1 1
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
       1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
       1
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
MOL
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
       1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)

%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)

%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)

%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)

%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)

%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)

%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)

%FLAG SOLTY
%FORMAT(5E16.8)
  0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  3.35544320E+06
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  1.63840000E+03
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)

%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)

%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)

%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)

%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)

%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)

%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
       0 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)

%FLAG HBOND_BCOEF
%FORMAT(5E16.8)

%FLAG HBCUT
%FORMAT(5E16.8)

%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
Se Cd
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
       0 0
%FLAG IROTAT
%FORMAT(10I8)
       0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
  1.50000000E+00 1.50000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
  8.00000000E-01 8.00000000E-01


logfile leap.log
cdse=loadpdb cdse.pdb
set cdse.0.1 type Se
set cdse.0.2 type Cd
set cdse.0.1 charge -0.6
set cdse.0.2 charge 0.6
loadamberparams cdse.frcmod
saveamberparm cdse cdse.prmtop cdse.inpcrd


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