[gmx-users] Own coarse-grained forcefield

[Justin Lemkul]

On 3/31/16 9:35 AM, Michał Kadlof wrote:
> 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
>

You're not assigning any bonds, so pdb2gmx doesn't write any bonds.

-Justin

> ==> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================