Anna Marabotti wrote:
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
The [defaults] directive can appear only once in a topology and must be the very
first entry. There is one in forcefield.itp and then you added another in your
ligand .itp file. That's why grompp complains.
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?
There is a very specific hierarchy that must be maintained in a topology. Force
field-level directives must appear before any molecules are declared, system
directives must follow all molecule declarations, etc.
You need the [atomtypes] directive for the topology to be valid, so keep it in
there and work with that topology. It seems to me that the order should be
correct, as shown, since the ligand's new [atomtypes] have to precede all
[moleculetype] directives. I have a similar case that I'm actually working on
right now that works fine, i.e.:
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
; Include ligand
#include "ligand.itp"
...then the protein stuff from pdb2gmx. The ligand.itp file contains an
[atomtypes] directive, which, in this position, is legal. Which version of
Gromacs are you using? If it's not 4.5.4, then I'll suggest that you upgrade
and try again. If it is 4.5.4, then check the contents of the ligand .itp file
carefully to make sure there aren't any remnants of the [defaults] directive
lying around.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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