[gmx-users] Own coarse-grained forcefield

[Michał Kadlof]

I would like to build my own coarse-grained forcefield for virtual beads-on-chain polymer. All I want for now is LJ Potential, and a spring between neighbours. Below are files that I have already have in my ff. The last file is my experimental structure in PDB format. When I run:

gmx pdb2gmx -f polimer10.pdb -o polimer10.gro

I got topol.top but there are no bonds.  What do I miss?





==> atomtypes.atp <==
B	1.00000	;	Simplest bead

==> beads.rtp <==
[ bondedtypes ]
; bonds	angles	dihedrals	impropers
1 1 1 1

[ BEA ]

[ atoms ]
; name	type charge	chargegroup
B	B	0.000	0

==> ffbonded.itp <==
[ bondtypes ]                                                                                             
; i j   func    b0  kb
B B 1   1   10000
[ angletypes ]
; i j k   func    th0 cth ub0 cub
B B B 1 180 10000

==> ffnonbonded.itp <==
[ atomtypes ]
;name   at.num  mass    charge  ptype   sigma   epsilon
B	1	1.00000	0.000	A	0.1	0.1

==> forcefield.doc <==
MYFORCEFIELD 	Very experimental forcefield

==> forcefield.itp <==

[ defaults ]
; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"

==> polimer10.pdb <==
ATOM      1  B   BEA A   1       0.000   0.000   0.000  0.00  0.00           C
ATOM      2  B   BEA A   2       1.000   0.000   0.000  0.00  0.00           C
ATOM      3  B   BEA A   3       2.000   0.000   0.000  0.00  0.00           C
ATOM      4  B   BEA A   4       3.000   0.000   0.000  0.00  0.00           C
ATOM      5  B   BEA A   5       4.000   0.000   0.000  0.00  0.00           C
ATOM      6  B   BEA A   6       5.000   0.000   0.000  0.00  0.00           C
ATOM      7  B   BEA A   7       6.000   0.000   0.000  0.00  0.00           C
ATOM      8  B   BEA A   8       7.000   0.000   0.000  0.00  0.00           C
ATOM      9  B   BEA A   9       8.000   0.000   0.000  0.00  0.00           C
ATOM     10  B   BEA A  10       9.000   0.000   0.000  0.00  0.00           C
TER      11      BEA A  11
CONECT    1    2
CONECT    2    1    3
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    6    8
CONECT    8    7    9
CONECT    9    8   10
CONECT   10    9

And here is the output of command.

$ gmx pdb2gmx -f polimer10.pdb -o polimer10.gro
(...)

GROMACS:      gmx pdb2gmx, VERSION 5.0.6
Executable:   /usr/bin/gmx
Library dir:  /usr/share/gromacs/top
Command line:
  gmx pdb2gmx -f polimer10.pdb -o polimer10.gro


Select the Force Field:
>From '/usr/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
(...)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: MYFORCEFILD	Very experimental forcefield
10: GROMOS96 43a1 force field
(...)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Using the myforcefield force field in directory myforcefield.ff

No file 'watermodels.dat' found, will not include a water model
Reading polimer10.pdb...
WARNING: all CONECT records are ignored
Read 10 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 10 atoms

  chain  #res #atoms
  1 'A'    10     10  

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/chromatine1.ff/atomtypes.atp
Atomtype 2
Reading residue database... (chromatine1)
Opening force field file /usr/share/gromacs/top/chromatine1.ff/beads.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Residue 1
Sorting it all out...

Processing chain 1 'A' (10 atoms, 10 residues)
Warning: Starting residue BEA1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA4 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA5 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 10 residues with 10 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are    0 dihedrals,    0 impropers,    0 angles
             0 pairs,        0 bonds and     0 virtual sites
Total mass 10.000 a.m.u.
Total charge 0.000 e
Writing topology