[gmx-users] problem in topology with AMBER99SB

Mon Sep 5 15:07:01 CEST 2011

Dear gmx-users,
I'm trying to create the topology for a ligand using Amber99SB force field,
but I'm experimenting several problems. Here what I did:
 - I recovered the .mol2 file of my ligand (comp1.mol2)
- I checked and added H with Amber tool reduce: reduce comp1.mol2 > comp1-H.
mol2
- I added charges using antechamber: antechamber -i comp1-H.mol2 -fi mol2 -o
comp1-H_C.mol2 -fo mol2 -c bcc -s2
- I created the frcmod parameter file: parmcheck -i comp1-H_C.mol2 -f mol2
-o comp1-H_C.frcmod 
- then I used: xleap -s -f /opt/amber11/dat/leap/cmd/leaprc.ff99SB
                            source leaprc.gaff
                            lig = loadmol2 comp1-H_C.mol2
                            check lig
                            loadamberparams comp1-H_C.frcmod
                            saveamberparm lig comp1.prmtop comp1.inpcrd
- I created the .top file with amb2gmx.pl: amb2gmx.pl --prmtop comp1.prmtop
--crd comp1.inpcrd --outname comp1
then
mv comp1.top comp1.itp

My comp1.itp file is as following:

; comp1.top created by rdparm2gmx.pl Mon Sep 5 12:45:09 CEST 2011

[ defaults ]

; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ

1 2 yes 0.5 0.8333

[ atomtypes ]

;name bond_type mass charge ptype sigma epsilon

c3 c3 0.0000 0.0000 A 3.39967e-01 4.57730e-01

n n 0.0000 0.0000 A 3.25000e-01 7.11280e-01

ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02

ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01

hn hn 0.0000 0.0000 A 1.06908e-01 6.56888e-02

hc hc 0.0000 0.0000 A 2.64953e-01 6.56888e-02

c c 0.0000 0.0000 A 3.39967e-01 3.59824e-01

o o 0.0000 0.0000 A 2.95992e-01 8.78640e-01

[ moleculetype ]

; Name nrexcl

solute 3

[ atoms ]

; nr type resnr residue atom cgnr charge mass typeB chargeB

1 o 1 UNK O1 1 -0.58510 16.000000

2 o 1 UNK O2 2 -0.47810 16.000000

3 o 1 UNK O3 3 -0.47710 16.000000

4 n 1 UNK N1 4 -0.47010 14.000000

............................................................................
...

[ bonds ]

; ai aj funct r k

4 33 1 1.0090e-01 3.4326e+05

7 26 1 1.0920e-01 2.8225e+05

7 25 1 1.0920e-01 2.8225e+05

7 24 1 1.0920e-01 2.8225e+05

............................................................................
...

[ pairs ]

; ai aj funct

1 33 1

4 36 1

4 34 1

5 33 1

............................................................................
...

[ angles ]

; ai aj ak funct theta cth

5 9 32 1 1.1005e+02 3.8802e+02

5 9 31 1 1.1005e+02 3.8802e+02

5 9 30 1 1.1005e+02 3.8802e+02

5 8 29 1 1.1005e+02 3.8802e+02

............................................................................
....

[ dihedrals ]

;i j k l func C0 ... C5

1 6 4 33 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ;

4 12 17 36 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;

4 12 14 34 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ;

5 6 4 33 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ;

6 5 9 32 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 ;

............................................................................
..

[ system ]

40 system

[ molecules ]

; Compound nmols

solute 1

I pasted the coordinates of comp1.pdb into those of protein.pdb, II removed
directives [ system ] and [ molecules ] and I included "comp1.itp" in the
"topol.top" file obtained with pdb2gmx (Gromacs 4.5.4) using ff Amber99SB,
on the protein alone:

topol.top:

; Include forcefield parameters

#include "amber99sb.ff/forcefield.itp"

#include "comp1.itp"

; Include chain topologies

#include "topol_Protein_chain_C.itp"

#include "topol_Other.itp"

; Include water topology

#include "amber99sb.ff/tip3p.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "amber99sb.ff/ions.itp"

[ system ]

; Name

Protein in water

[ molecules ]

; Compound #mols

Protein_chain_C 1

Other 1

UNK 1

Then, I launched editconf-genbox-grompp to neutralize system:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

The result was:

Fatal error:

Syntax error - File comp1.itp, line 3

Last line read:

'[ defaults ]'

Invalid order for directive defaults

I had a check on the manual and it seems to me that all directives are in
the correct order! However, I removed directive [ defaults ] and re-launched
grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

Result:

Fatal error:

Syntax error - File comp1.itp, line 7

Last line read:

'[ atomtypes ]'

Invalid order for directive atomtypes

I removed directive [ atomtypes ] and re-launched grompp:

/opt/gromacs45/bin/grompp -f em.mdp -c prot-lig_solv.gro -o
prot-lig_solv.tpr -p

Result:

Fatal error:

Atomtype n not found

What's wrong? Why Gromacs claims that directives are not in correct order?
Could you please help me?

Many thanks

Anna

__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm

"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)

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