lonepair (c39b1)
Lone Pair Facility
This routine parses the lone-pair command which converts existing
atoms to lone-pairs in the PSF.
Bernard R. Brooks, NIH, October, 1997
* Syntax | Syntax of the lone-pair command
* Description | Description of the lone-pair facility
This routine parses the lone-pair command which converts existing
atoms to lone-pairs in the PSF.
Bernard R. Brooks, NIH, October, 1997
* Syntax | Syntax of the lone-pair command
* Description | Description of the lone-pair facility
Top
Syntax of the Lone-Pait Command
[SYNTAX LONEpair]
LONEpair { FIXEd atom-spec [ xloc-yloc-zloc ] } [MASS]
{ }
{ CENTer atom-spec { atom-selection } }
{ { repeat(atom-spec) } }
{ }
{ COLOcate { 2x(atom-selection) } }
{ { 2x(atom-spec) } }
{ }
{ { COLInear distance-spec } { 3x(atom-selection) } }
{ { CEN2 } { 3x(atom-spec) } }
{ }
{ { RELAtive } { 4x(atom-selection) } position-spec }
{ { BISEctor } { 4x(atom-selection) } }
{ { CEN3 } }
{ }
{ PRINt }
{ CLEAr [MASS real] }
atom-spec::= { residue-number atom-name }
{ segid resid atom-name }
{ BYNUm atom-number }
atom-selection ::= » select .
xloc-yloc-zloc::= three real numbers identifying the new position
distance-spec::= [DISTance real] [SCAled real]
(def 0.0) (def 0.0)
postition-spec::= [DISTance real] [ANGLe real] [DIHEdral real]
(def 0.0) (def 0.0) (def 0.0)
Syntax of the Lone-Pait Command
[SYNTAX LONEpair]
LONEpair { FIXEd atom-spec [ xloc-yloc-zloc ] } [MASS]
{ }
{ CENTer atom-spec { atom-selection } }
{ { repeat(atom-spec) } }
{ }
{ COLOcate { 2x(atom-selection) } }
{ { 2x(atom-spec) } }
{ }
{ { COLInear distance-spec } { 3x(atom-selection) } }
{ { CEN2 } { 3x(atom-spec) } }
{ }
{ { RELAtive } { 4x(atom-selection) } position-spec }
{ { BISEctor } { 4x(atom-selection) } }
{ { CEN3 } }
{ }
{ PRINt }
{ CLEAr [MASS real] }
atom-spec::= { residue-number atom-name }
{ segid resid atom-name }
{ BYNUm atom-number }
atom-selection ::= » select .
xloc-yloc-zloc::= three real numbers identifying the new position
distance-spec::= [DISTance real] [SCAled real]
(def 0.0) (def 0.0)
postition-spec::= [DISTance real] [ANGLe real] [DIHEdral real]
(def 0.0) (def 0.0) (def 0.0)
Top
Note on the lone-pair command
1. The "LONEpair FIXEd" command places atoms that are fixed in
the unit cell fractional coordinates. If running constant pressure,
these atoms will move in response to the changes in the box size/shape.
Thus, this is different than "CONStraint FIX". The specified position
is in cartesian space (Angstroms).
2. The "LONEpair CENTer" command places a single particle at the
weighted center of all the subsequently specified atoms (either by
atom-selection or atom-spec).
3. For all commands employing multiple atom selections, each atom
selection MUST CONTAIN THE SAME NUMBER OF ATOMS. The atoms are
then matched off in sequential order. The first atom selection is
the list of lonepair atoms. This is intended to make it easy
to create a large number of TIP4P water molecules with one command:
LONEpair BISEctor DIST 0.15 ANGLE 0.0 DIHE 0.0 -
SELE ATOM SOLV * OM END -
SELE ATOM SOLV * OH2 END -
SELE ATOM SOLV * H1 END -
SELE ATOM SOLV * H2 END
This assumes that all of the residues in the segment SOLV are TIP4P
types. It places the atom OM (with zero mass) at a point 0.15 A
from the atom OH2 in the direction of the H1-H2 bisector.
4. The MASS option is used in the CEN* commands to determine how the
center position is computed. The default is to use the center of
geometry (unit weights for all atoms).
5. The CLEAr command will remove all lone-pairs from the PSF and
resets the lone-pair facility. WARNING: The masses of old lone-pairs
will still be zero. These may be modified "SCALAR MASS SET..."
before running further dynamics, or by using the MASS keyword value
whereby the mass of removed lonepairs are assigned to this value.
6. Lone-pair atoms may have other lone-pair atoms as a host, provided
that the host is not already a lonepair. In other words, you can define
the postition of lone-pair B based on the postition of lone-pair A
ONLY if lonepair B is define before lonepair A. ORDER IS IMPORTANT!!
7. The LONEpair command sets the MASS to zero of all selected
lone-pairs. This MAY change the total mass of the system. The
lost mass is NOT added to any other atom.
8. For the BISEctor option, the dihedral is based on: I,J,(K+L)/2,L
where I,J,K,L are the coordinate vectors of the specified atoms.
9. For the COLInear option, the DISTance value is a signed value
of the distance from the first host AWAY from the second host.
The SCALed value is a relative distance from the first atoms AWAY
from the second atom (a SCALed factor of -1.0 will put the lonepair
at the position of the second atom). For example, the following
two commands do exactly the same thing:
LONEpair COLINEAR DIST 0.0 SCALE -0.5 -
SELE type HB END SELE type H1 END SELE type H2 END
LONEpair CEN2 -
SELE type HB END SELE type H1 END SELE type H2 END
10. When running CHARMM in parallel, the lonepair atom should be in
the same group as ALL of its hosts in order to ensure that these
atoms are all in the same parallel partition. THIS IS NOT CHECKED!
11. Lonepair data is considered to be part of the PSF. When a PSF
with lonepairs is read from a file, the lonepair facility is also
read (or appended).
12. When using lonepairs with PERT, both PSF's MUST have the same
lonepair data. In other words, you cannot perturb a lonepair into
a non-lonepair.
13. Lone pairs may now be set in the RTF using a syntax similar to the
standard lonepair command » lonepair . All options for the
generation of lonepairs (FIXed, CENTer, COLOcate etc.) as specified
in the lonepair documentation may be used although the atom selection
specification is simplied as shown in the following example.
LONEPAIR relative LPA O C CL distance 0.3 angle 91.0 dihe 0.0
LONEPAIR relative LPB O C N distance 0.3 angle 91.0 dihe 0.0
14. Lone pairs with undefined coordinates can be built by COOR SHAKE.
Note on the lone-pair command
1. The "LONEpair FIXEd" command places atoms that are fixed in
the unit cell fractional coordinates. If running constant pressure,
these atoms will move in response to the changes in the box size/shape.
Thus, this is different than "CONStraint FIX". The specified position
is in cartesian space (Angstroms).
2. The "LONEpair CENTer" command places a single particle at the
weighted center of all the subsequently specified atoms (either by
atom-selection or atom-spec).
3. For all commands employing multiple atom selections, each atom
selection MUST CONTAIN THE SAME NUMBER OF ATOMS. The atoms are
then matched off in sequential order. The first atom selection is
the list of lonepair atoms. This is intended to make it easy
to create a large number of TIP4P water molecules with one command:
LONEpair BISEctor DIST 0.15 ANGLE 0.0 DIHE 0.0 -
SELE ATOM SOLV * OM END -
SELE ATOM SOLV * OH2 END -
SELE ATOM SOLV * H1 END -
SELE ATOM SOLV * H2 END
This assumes that all of the residues in the segment SOLV are TIP4P
types. It places the atom OM (with zero mass) at a point 0.15 A
from the atom OH2 in the direction of the H1-H2 bisector.
4. The MASS option is used in the CEN* commands to determine how the
center position is computed. The default is to use the center of
geometry (unit weights for all atoms).
5. The CLEAr command will remove all lone-pairs from the PSF and
resets the lone-pair facility. WARNING: The masses of old lone-pairs
will still be zero. These may be modified "SCALAR MASS SET..."
before running further dynamics, or by using the MASS keyword value
whereby the mass of removed lonepairs are assigned to this value.
6. Lone-pair atoms may have other lone-pair atoms as a host, provided
that the host is not already a lonepair. In other words, you can define
the postition of lone-pair B based on the postition of lone-pair A
ONLY if lonepair B is define before lonepair A. ORDER IS IMPORTANT!!
7. The LONEpair command sets the MASS to zero of all selected
lone-pairs. This MAY change the total mass of the system. The
lost mass is NOT added to any other atom.
8. For the BISEctor option, the dihedral is based on: I,J,(K+L)/2,L
where I,J,K,L are the coordinate vectors of the specified atoms.
9. For the COLInear option, the DISTance value is a signed value
of the distance from the first host AWAY from the second host.
The SCALed value is a relative distance from the first atoms AWAY
from the second atom (a SCALed factor of -1.0 will put the lonepair
at the position of the second atom). For example, the following
two commands do exactly the same thing:
LONEpair COLINEAR DIST 0.0 SCALE -0.5 -
SELE type HB END SELE type H1 END SELE type H2 END
LONEpair CEN2 -
SELE type HB END SELE type H1 END SELE type H2 END
10. When running CHARMM in parallel, the lonepair atom should be in
the same group as ALL of its hosts in order to ensure that these
atoms are all in the same parallel partition. THIS IS NOT CHECKED!
11. Lonepair data is considered to be part of the PSF. When a PSF
with lonepairs is read from a file, the lonepair facility is also
read (or appended).
12. When using lonepairs with PERT, both PSF's MUST have the same
lonepair data. In other words, you cannot perturb a lonepair into
a non-lonepair.
13. Lone pairs may now be set in the RTF using a syntax similar to the
standard lonepair command » lonepair . All options for the
generation of lonepairs (FIXed, CENTer, COLOcate etc.) as specified
in the lonepair documentation may be used although the atom selection
specification is simplied as shown in the following example.
LONEPAIR relative LPA O C CL distance 0.3 angle 91.0 dihe 0.0
LONEPAIR relative LPB O C N distance 0.3 angle 91.0 dihe 0.0
14. Lone pairs with undefined coordinates can be built by COOR SHAKE.