[gmx-users] Creating a new topology using OPLSAA
Mike Wykes
wykesm at averell.umh.ac.be
Fri Aug 1 11:49:33 CEST 2008
Dear Gromacs Users
I would like to use Gromacs to perform MD on polymers using the OPLSAA
FF. After reading the section of the manual on file formats, I decided
it would be best to create a residue topology file (.rtp) for the
monomer along with a pdb file with the corresponding residue name. After
adding the residue definition to aminoacids.dat I was able to use
pdb2gmx to generate my .gro and .top files. The benefit of creating an
rtp file is that I could easily create .gro and .top files for a larger
molecule of eg. 100 monomers from a pdb containing 100 monomers.
To begin with, I started with a very simple case, namely creating
biphenyl from a pdb containing two of my own phenyl monomer residues and
their rtp file (shown below). In the resulting top file I noticed that
the bonds, pairs, angles and dihedrals parameters were all blank.
However the improper dihedrals had the placeholders (e.g.
improper_Z_CA_X_Y) which I manually defined in the rtp file.
Being unfamiliar with the way in which grompp works, I thought perhaps
the missing parameters would be added by grompp as it would have all the
necessary atom type definitions and interaction types to assign each
interaction parameter. So I ran grompp and asked for a processed
topology file using the -pp option. Initially it complained that some
dihedrals were missing from the oplsa ff, so I added them to
ffoplsaabon.itp using analogous parameters. Then it ran without
complaining but still the parameters for bonds, pairs, angles and
dihedrals parameters were missing in the resulting .top file. However
the place holders for the improper dihedrals had been replaced with
actual parameters.
I looked at the tutorial on speptide and generated the topology using
the ffG43a1 FF and saw that this has place holders for each bonded
interaction eg gb_2 in the top file which grompp then replaces with
parameters found in the corresponding #define statement in the .itp
force field file. running grompp on this top results in a topology file
with bond, angle etc parameters for every interaction. I ran pdb2gmx on
the speptide pdb this time selecting OPLSAA as the FF and again the
bonded interaction parameters were missing, except when a dihedral had
specifically been defined as in e.g. LYS. The placeholder
dih_LYS_chi1_N_C_C_C was replaced by actual parameters when I ran grompp
asking for a processed topology file.
So are the ffG3a1 and OPLSAA force fields just implemented differently
or should there be parameters for all the bonded interactions in my
grompp-processed topology file? Or does it not matter that the
parameters are blank, since the atom types and bonded interaction types
can be used to define the parameters for each interaction?
Thanks in advance
Mike
Here is my monomer rtp file:
[ PHEN ]
[ atoms ]
C opls_145B 0.0 1
C2 opls_145 -0.115 2
HC2 opls_146 0.115 2
C3 opls_145 -0.115 3
HC3 opls_146 0.115 3
C4 opls_145B 0.0 4
C5 opls_145 -0.115 5
HC5 opls_146 0.115 5
C6 opls_145 -0.115 6
HC6 opls_146 0.115 6
[ bonds ]
C C2
C2 HC2
C2 C3
C3 HC3
C3 C4
C4 C5
C5 HC5
C5 C6
C6 HC6
C6 C
+C C4
[ impropers ]
C4 C6 C5 HC5 improper_Z_CA_X_Y
C5 C C6 HC6 improper_Z_CA_X_Y
C6 C2 C -C4 improper_Z_CA_X_Y
C C3 C2 HC2 improper_Z_CA_X_Y
C2 C4 C3 HC3 improper_Z_CA_X_Y
C3 C5 C4 -C improper_Z_CA_X_Y
here is my topology file:
;
; File 'biphenyl.top' was generated
; By user: wykesm (1002)
; On host: debian
; At date: Thu Jul 31 15:29:10 2008
;
; This is your topology file
; "It's So Fast It's Slow" (F. Black)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_145B 1 PHEN C 1 0 12.011 ;
qtot 0
2 opls_145 1 PHEN C2 2 -0.115 12.011 ;
qtot -0.115
3 opls_146 1 PHEN HC2 2 0.115 1.008 ;
qtot 0
4 opls_145 1 PHEN C3 3 -0.115 12.011 ;
qtot -0.115
5 opls_146 1 PHEN HC3 3 0.115 1.008 ;
qtot 0
6 opls_145B 1 PHEN C4 4 0 12.011 ;
qtot 0
7 opls_145 1 PHEN C5 5 -0.115 12.011 ;
qtot -0.115
8 opls_146 1 PHEN HC5 5 0.115 1.008 ;
qtot 0
9 opls_145 1 PHEN C6 6 -0.115 12.011 ;
qtot -0.115
10 opls_146 1 PHEN HC6 6 0.115 1.008 ;
qtot 0
11 opls_145B 2 PHEN C 7 0 12.011 ;
qtot 0
12 opls_145 2 PHEN C2 8 -0.115 12.011 ;
qtot -0.115
13 opls_146 2 PHEN HC2 8 0.115 1.008 ;
qtot 0
14 opls_145 2 PHEN C3 9 -0.115 12.011 ;
qtot -0.115
15 opls_146 2 PHEN HC3 9 0.115 1.008 ;
qtot 0
16 opls_145B 2 PHEN C4 10 0 12.011 ;
qtot 0
17 opls_145 2 PHEN C5 11 -0.115 12.011 ;
qtot -0.115
18 opls_146 2 PHEN HC5 11 0.115 1.008 ;
qtot 0
19 opls_145 2 PHEN C6 12 -0.115 12.011 ;
qtot -0.115
20 opls_146 2 PHEN HC6 12 0.115 1.008 ;
qtot 0
[ bonds ]
; ai aj funct c0 c1 c2
c3
1 2 1
1 9 1
2 3 1
2 4 1
4 5 1
4 6 1
6 7 1
6 11 1
7 8 1
7 9 1
9 10 1
11 12 1
11 19 1
12 13 1
12 14 1
14 15 1
14 16 1
16 17 1
17 18 1
17 19 1
19 20 1
[ pairs ]
; ai aj funct c0 c1 c2
c3
1 5 1
1 6 1
1 8 1
2 7 1
2 10 1
2 11 1
3 5 1
3 6 1
3 9 1
4 8 1
4 9 1
4 12 1
4 19 1
5 7 1
5 11 1
6 10 1
6 13 1
6 14 1
6 17 1
6 20 1
7 12 1
7 19 1
8 10 1
8 11 1
9 11 1
11 15 1
11 16 1
11 18 1
12 17 1
12 20 1
13 15 1
13 16 1
13 19 1
14 18 1
14 19 1
15 17 1
16 20 1
18 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 9 1
1 2 3 1
1 2 4 1
3 2 4 1
2 4 5 1
2 4 6 1
5 4 6 1
4 6 7 1
4 6 11 1
7 6 11 1
6 7 8 1
6 7 9 1
8 7 9 1
1 9 7 1
1 9 10 1
7 9 10 1
6 11 12 1
6 11 19 1
12 11 19 1
11 12 13 1
11 12 14 1
13 12 14 1
12 14 15 1
12 14 16 1
15 14 16 1
14 16 17 1
16 17 18 1
16 17 19 1
18 17 19 1
11 19 17 1
11 19 20 1
17 19 20 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
9 1 2 3 3
9 1 2 4 3
2 1 9 7 3
2 1 9 10 3
1 2 4 5 3
1 2 4 6 3
3 2 4 5 3
3 2 4 6 3
2 4 6 7 3
2 4 6 11 3
5 4 6 7 3
5 4 6 11 3
4 6 7 8 3
4 6 7 9 3
11 6 7 8 3
11 6 7 9 3
4 6 11 12 3
4 6 11 19 3
7 6 11 12 3
7 6 11 19 3
6 7 9 1 3
6 7 9 10 3
8 7 9 1 3
8 7 9 10 3
6 11 12 13 3
6 11 12 14 3
19 11 12 13 3
19 11 12 14 3
6 11 19 17 3
6 11 19 20 3
12 11 19 17 3
12 11 19 20 3
11 12 14 15 3
11 12 14 16 3
13 12 14 15 3
13 12 14 16 3
12 14 16 17 3
15 14 16 17 3
14 16 17 18 3
14 16 17 19 3
16 17 19 11 3
16 17 19 20 3
18 17 19 11 3
18 17 19 20 3
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
1 4 2 3 1 improper_Z_CA_X_Y
1 16 17 14 1 improper_Z_CA_X_Y
2 6 4 5 1 improper_Z_CA_X_Y
6 9 7 8 1 improper_Z_CA_X_Y
6 11 12 19 1 improper_Z_CA_X_Y
7 1 9 10 1 improper_Z_CA_X_Y
11 14 12 13 1 improper_Z_CA_X_Y
12 16 14 15 1 improper_Z_CA_X_Y
16 19 17 18 1 improper_Z_CA_X_Y
17 11 19 20 1 improper_Z_CA_X_Y
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1
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