Handling topologies of non-standard molecules in Gromacs

I have a file containing a protein chain and a non-standard ligand in a file [centered.pdb]. To obtain .top file
create a directory in the workspace and call it forcefield.ff.

export GMXLIB=$GMXLIB:$PWD/

The contents of that directory are:


ls -1 forcefield.ff/
aminoacids.c.tdb
aminoacids.hdb
aminoacids.n.tdb
aminoacids.r2b
aminoacids.rtp
aminoacids.vsd
atomtypes.atp
b12rtp
elements.dat
ffbonded.itp
ff_dum.itp
ffG53a6.itp
ffnonbonded.itp
forcefield.doc
forcefield.itp
gromos53a6.ff
ions.itp
old
org-aminoacidsrtp
spce.itp
spc.itp
tip3p.itp
tip4p.itp
watermodels.dat

The file aminoacids.itp has these lines added at the end:

[ Ligand ]
[ atoms ]
C27     C       0.38000 0 ; from        GLN     residue
O28     O       -0.38000 0 ; from       GLN     residue
N29     NT      -0.83000 0 ; from       GLN     residue
..

[ bonds ]
; ai aj gromos type
C26     C27 gb_27 ; from        GLN     fragment 0
C27     O28 gb_5 ; from GLN
C27     N29 gb_9 ; from GLN
...

[ dihedrals ]
; ai aj ak al gromos type
C3R     O2      P       O3 gd_20 ; from ADE     phosphate definition
C3R     O2      P       O3 gd_27 ; from ADE     phosphate definition
C2P     O3      P       O2 gd_20 ; from ADE     phosphate definition...

Then...

 pdb2gmx_sp -f centered.pdb  -o centered.pg.gro
...


Select the Force Field:
From current directory:
 1: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
From '/usr/common/usg/gromacs/4.6.1-sp/share/gromacs/top':
 2: AMBER03 protein, nucleic AMBER94 (Duan et al.,.. 24, 1999-2012, 2003)
 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
...

16: [DEPRECATED] Encad all-atom force field, using full solvent charges
17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
18: [DEPRECATED] Gromacs force field (see manual)
19: [DEPRECATED] Gromacs force field with hydrogens for NMR

Select 1 which is the forcefield contained in the directory forcefield.ff. This should run w/o errors and give a topol.top file. W/o editing topol.top running this code will give the following error;

grompp_sp -f min.mdp -c centered.pg.gro -p topol.top -o em.tpr
...

-------------------------------------------------------
Program grompp_sp, VERSION 4.6.1
Source code file: /global/homes/j/jdeslip/Builds/Hopper/gromacs-4.6.1/src/kernel/topio.c, line: 734

Fatal error:
Syntax error - File ffnonbonded.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

So, hide the first line and add the default gromos53a6.ff

;#include "./forcefield.ff/forcefield.itp"

#include "gromos53a6.ff/forcefield.itp"

That should let grompp run smoothly.