mndo97 (c39b1)
Combined Quantum Mechanical and Molecular Mechanics Method
Based on MNDO97 in CHARMM
by Paul Bash (pabash@nwu.edu)
Additional modifications
Kwangho Nam(nam@chem.umn.edu) and Darrin York
* Description | Description of the MNDO97 commands
* Usage | How to run MNDO97 in CHARMM
* NEWD | NEWD Command
* Installation | How to install MNDO97 in CHARMM environment
Based on MNDO97 in CHARMM
by Paul Bash (pabash@nwu.edu)
Additional modifications
Kwangho Nam(nam@chem.umn.edu) and Darrin York
* Description | Description of the MNDO97 commands
* Usage | How to run MNDO97 in CHARMM
* NEWD | NEWD Command
* Installation | How to install MNDO97 in CHARMM environment
Top
The MNDO97 QM potential is initialized with the MNDO97 command.
[SYNTAX MNDO97]
MNDO97 [REMOve] [EXGRoup] (atom selection) [UNIT int]
[GLNK atom-selection]
[NEWD int] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer
{ KMXX integer KMXY integer KMXZ integer }
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
UNIT: Fortran unit for MNDO97 input file. (refere following example)
GLNK: GHO method implementation (refer qmmm.doc).
The syntax of the MNDO97 command in CHARMM follows closely that
of the GAMESS command.
The MNDO97 QM potential is initialized with the MNDO97 command.
[SYNTAX MNDO97]
MNDO97 [REMOve] [EXGRoup] (atom selection) [UNIT int]
[GLNK atom-selection]
[NEWD int] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer
{ KMXX integer KMXY integer KMXZ integer }
REMOve: Classical energies within QM atoms are removed.
EXGRoup: QM/MM Electrostatics for link host groups removed.
UNIT: Fortran unit for MNDO97 input file. (refere following example)
GLNK: GHO method implementation (refer qmmm.doc).
The syntax of the MNDO97 command in CHARMM follows closely that
of the GAMESS command.
Top
For complete information about MNDO97 input see MNDO97 documentation.
A QM-MM job using MNDO97 needs two input files. The first is the
normal CHARMM input file containing the MNDO97 command. The second file is
the normal MNDO97 input file.
Mndo97 Input File
-----------------
For the MNDO97 input file all the keywords are required as for a stand
alone MNDO97 calculation. The CHARMM minimizer is used so an MNDO97
run with only an energy and gradient calculation is necessary.
Examples
--------
An example of a MNDO97 input file to run with CHARMM: (for example, this file
named as "mndo.inp")
iop=0 jop=-2 iform=2 igeom=1 + kharge=0 nprint=-5 mprint=-5
mminp=2 numatm=7 mmcoup=2 mmpot=7 mmfile=-1 ipsana=1
LYSINE
86 84.122 1 39.595 1 47.383 1
6 84.879 1 40.615 1 46.561 1
1 84.209 1 41.474 1 46.345 1
1 85.187 1 40.149 1 45.601 1
6 86.125 1 41.126 1 47.288 1
1 86.886 1 40.317 1 47.281 1
1 85.845 1 41.349 1 48.339 1
6 86.761 1 42.385 1 46.686 1
1 86.016 1 43.208 1 46.649 1
1 87.116 1 42.176 1 45.654 1
6 87.922 1 42.778 1 47.563 1
1 88.790 1 42.117 1 47.353 1
1 87.628 1 42.695 1 48.631 1
7 88.359 1 44.196 1 47.319 1
1 87.569 1 44.842 1 47.519 1
1 88.652 1 44.303 1 46.327 1
0 0.0000000000 0 0.0000000000 0 0.0000000000 0
See the documentation for MNDO97 for a description of the MNDO97 keywords.
Each atom to be treated QM MUST be listed explicity in this MNDO97
input file. They MUST be in the same order as the CHARMM coordinate file.
MNDO97 is called the first time using this input file and coordinates,
and does an initial setup and calculates one energy and gradient.
Subsequent energy and force calculations use coordinates from CHARMM
data structures. Atom "86" above is a special "link" termination atom,
which may be used instead of a hydrogen. This may work better in some
instances than a hydrogen. Atom 86 is only parameterized for C-C single
bond.
Current implementation has a limit is choosing non-bonded options. All
atom based cutoffs methods is not fully supported for a certain boundary
conditions such as periodic boundary condition. In any case, the QM-MM
non-bond generation routine will only generate the non-bond list based
on group-group separation scheme. Especially to use any periodic boundary
conditions, it is strongly recomented to use group based cutoff scheme.
A sample shell script to run CHARMM with MNDO97 is:
* Y160F simulation with NHDP isocitrate
! open topology and parameter files
open unit 10 form read name top_all22_prot_na.inp
read rtf card unit 10
close unit 10
open unit 11 form read name par_all22_prot_na.inp
read param card unit 11
close unit 11
bomb -3
! open appropriate coordinate file
open unit 12 form read name lysn.pdb
read sequ coor resi pdb unit 12
rewind unit 12
generate 7tim first none last none setup warn
read coor resi pdb unit 12
close unit 12
update
! Before call MNDO command, MNDO97 input file should be opened
! and the unit of that file should be specified in MNDO command.
! call the MNDO command
! initial setup energy and gradient calculation
! It is possible at this point to run MNDO97 stand alone
! by changing the MNDO97 input to do a geometry optimization
! One would want to place a "stop" command after this command.
open read unit 66 form name mndo.inp
mndo unit 66 sele all end remo
! calculate the energy using coordinates from CHARMM
energy
! do an energy minimization
mini abnr nstep 500 nprint 1
! write out coordinates
open unit 22 form write name lysn_min.pdb
write coor pdb unit 22
* water
close unit 22
stop
To run MNDO97/CHARMM one may use the following script:
At the moment, MNDO97's input file needs to be opened before call MNDO.
For complete information about MNDO97 input see MNDO97 documentation.
A QM-MM job using MNDO97 needs two input files. The first is the
normal CHARMM input file containing the MNDO97 command. The second file is
the normal MNDO97 input file.
Mndo97 Input File
-----------------
For the MNDO97 input file all the keywords are required as for a stand
alone MNDO97 calculation. The CHARMM minimizer is used so an MNDO97
run with only an energy and gradient calculation is necessary.
Examples
--------
An example of a MNDO97 input file to run with CHARMM: (for example, this file
named as "mndo.inp")
iop=0 jop=-2 iform=2 igeom=1 + kharge=0 nprint=-5 mprint=-5
mminp=2 numatm=7 mmcoup=2 mmpot=7 mmfile=-1 ipsana=1
LYSINE
86 84.122 1 39.595 1 47.383 1
6 84.879 1 40.615 1 46.561 1
1 84.209 1 41.474 1 46.345 1
1 85.187 1 40.149 1 45.601 1
6 86.125 1 41.126 1 47.288 1
1 86.886 1 40.317 1 47.281 1
1 85.845 1 41.349 1 48.339 1
6 86.761 1 42.385 1 46.686 1
1 86.016 1 43.208 1 46.649 1
1 87.116 1 42.176 1 45.654 1
6 87.922 1 42.778 1 47.563 1
1 88.790 1 42.117 1 47.353 1
1 87.628 1 42.695 1 48.631 1
7 88.359 1 44.196 1 47.319 1
1 87.569 1 44.842 1 47.519 1
1 88.652 1 44.303 1 46.327 1
0 0.0000000000 0 0.0000000000 0 0.0000000000 0
See the documentation for MNDO97 for a description of the MNDO97 keywords.
Each atom to be treated QM MUST be listed explicity in this MNDO97
input file. They MUST be in the same order as the CHARMM coordinate file.
MNDO97 is called the first time using this input file and coordinates,
and does an initial setup and calculates one energy and gradient.
Subsequent energy and force calculations use coordinates from CHARMM
data structures. Atom "86" above is a special "link" termination atom,
which may be used instead of a hydrogen. This may work better in some
instances than a hydrogen. Atom 86 is only parameterized for C-C single
bond.
Current implementation has a limit is choosing non-bonded options. All
atom based cutoffs methods is not fully supported for a certain boundary
conditions such as periodic boundary condition. In any case, the QM-MM
non-bond generation routine will only generate the non-bond list based
on group-group separation scheme. Especially to use any periodic boundary
conditions, it is strongly recomented to use group based cutoff scheme.
A sample shell script to run CHARMM with MNDO97 is:
* Y160F simulation with NHDP isocitrate
! open topology and parameter files
open unit 10 form read name top_all22_prot_na.inp
read rtf card unit 10
close unit 10
open unit 11 form read name par_all22_prot_na.inp
read param card unit 11
close unit 11
bomb -3
! open appropriate coordinate file
open unit 12 form read name lysn.pdb
read sequ coor resi pdb unit 12
rewind unit 12
generate 7tim first none last none setup warn
read coor resi pdb unit 12
close unit 12
update
! Before call MNDO command, MNDO97 input file should be opened
! and the unit of that file should be specified in MNDO command.
! call the MNDO command
! initial setup energy and gradient calculation
! It is possible at this point to run MNDO97 stand alone
! by changing the MNDO97 input to do a geometry optimization
! One would want to place a "stop" command after this command.
open read unit 66 form name mndo.inp
mndo unit 66 sele all end remo
! calculate the energy using coordinates from CHARMM
energy
! do an energy minimization
mini abnr nstep 500 nprint 1
! write out coordinates
open unit 22 form write name lysn_min.pdb
write coor pdb unit 22
* water
close unit 22
stop
To run MNDO97/CHARMM one may use the following script:
At the moment, MNDO97's input file needs to be opened before call MNDO.
Top
Description of the NEWE Command
[ NEWD int ] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer
{ KMXX integer KMXY integer KMXZ integer }
A simple Ewald sum method is implemented into the QM/MM potential. A full
description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2.
This is based on regular Ewald sum method and share similar keywords
(» ewald ).
The defaults for the QM/MM-Ewald calculations are set internallya and are
currently set to NEWD -1, KMAX=5, KSQMax=27, where the KMAX keyword is the
number of kvectors (or images of the primary unit cell) that will be summed
in any direction. It is the radius of the Ewald summation. For orthorombic
cells, the value of kmax may be independently specified in the x, y, and z
directions with the keywords KMXX, KMXY, and KMXZ. But, different from
regular Ewald in CHARMM, it has no limitation on the shape of box, and can be
used with PMEwald in MM part.
The KSQMax key word should be chosen between KMAX squared and 3 times
KMAX squared, and KAPPA value share the exact same number you use in Nonbond
options.
Description of the NEWE Command
[ NEWD int ] ewald-spec
ewald-spec::= { [ KMAX integer ] } KSQMAX integer
{ KMXX integer KMXY integer KMXZ integer }
A simple Ewald sum method is implemented into the QM/MM potential. A full
description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2.
This is based on regular Ewald sum method and share similar keywords
(» ewald ).
The defaults for the QM/MM-Ewald calculations are set internallya and are
currently set to NEWD -1, KMAX=5, KSQMax=27, where the KMAX keyword is the
number of kvectors (or images of the primary unit cell) that will be summed
in any direction. It is the radius of the Ewald summation. For orthorombic
cells, the value of kmax may be independently specified in the x, y, and z
directions with the keywords KMXX, KMXY, and KMXZ. But, different from
regular Ewald in CHARMM, it has no limitation on the shape of box, and can be
used with PMEwald in MM part.
The KSQMax key word should be chosen between KMAX squared and 3 times
KMAX squared, and KAPPA value share the exact same number you use in Nonbond
options.
Top
MNDO97/CHARMM interface status (February 1997)
- MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat
- The program runs on GNU, SGI, ALTIX, and IBMSP machines.
To compile MNDO97 with CHARMM one uses:
install.com [machine] [size] W
The "W" specifies to compile and link MNDO97 with CHARMM. The MNDO97
code MUST be in a subdirectory called "mndo97q" that resides in
$chmroot/source/mndint. mndint.src contains the QM/MM interface code.
It is similar to cadint.src and gamint.src.
In $chmroot/source/mndint/mndo97q are files such as irixx.mak, aix4.mak,
and etc. These files must be linked to machine.mak in order for the mndo97
code to compile properly for a given machine. For example, on the IBMSP
aix4.mak was used to compile the code. install.com is already set up
to make this link for both an IBMSP, GNU, ALTIX, and SGI. See install.com
for details and to make changes for other machines. Also, located in
$chmroot/source/mndint/mndo97q is a file called "changes_qmmm". This
file lists changes made to the original mndo97 code required due
primarily to conflicts with variable names in CHARMM. These variables
may be changes in subsequent versions of MNDO97.
Note on GNU machine, before start compiling the program, the compiler
should be determined and modify source/mndint/mndo97q/gnu.mak file
correspondingly. Otherwise, the error will occur. Currently, several
compilers are tested, including g77 and ifort.
MNDO97/CHARMM interface status (February 1997)
- MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat
- The program runs on GNU, SGI, ALTIX, and IBMSP machines.
To compile MNDO97 with CHARMM one uses:
install.com [machine] [size] W
The "W" specifies to compile and link MNDO97 with CHARMM. The MNDO97
code MUST be in a subdirectory called "mndo97q" that resides in
$chmroot/source/mndint. mndint.src contains the QM/MM interface code.
It is similar to cadint.src and gamint.src.
In $chmroot/source/mndint/mndo97q are files such as irixx.mak, aix4.mak,
and etc. These files must be linked to machine.mak in order for the mndo97
code to compile properly for a given machine. For example, on the IBMSP
aix4.mak was used to compile the code. install.com is already set up
to make this link for both an IBMSP, GNU, ALTIX, and SGI. See install.com
for details and to make changes for other machines. Also, located in
$chmroot/source/mndint/mndo97q is a file called "changes_qmmm". This
file lists changes made to the original mndo97 code required due
primarily to conflicts with variable names in CHARMM. These variables
may be changes in subsequent versions of MNDO97.
Note on GNU machine, before start compiling the program, the compiler
should be determined and modify source/mndint/mndo97q/gnu.mak file
correspondingly. Otherwise, the error will occur. Currently, several
compilers are tested, including g77 and ifort.