Hi
I want to generate the force field for a ligand and combine it with my
macromolecule to perform an MD simulation. I have done the following:
I am using AMBER8.
I have generated a .prep file for my ligand (2OG) using antechamber
Next i used parmchk to see if there are any missing parameters and the resulting
frcmod file looked like this:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON
So i assumed that there are no missing parameters.
Next i loaded my .prep and .frcmod file to leap and used the following script
to generate the topology file for my macromolecule+ligand (pdb named 1EA0_A.pdb
in the script and my ligand is named 2OG):
loadAmberParams 2OG.frcmod
loadAmberPrep 2OG.prep
1ea0 = loadpdb 1EA0_A.pdb
addions 1ea0 Na+ 0
solvatebox 1ea0 TIP3PBOX 10.00 0.75
saveamberparm 1ea0 1ea0.prm.top 1ea0.prm.crd
quit
I have the following output:
----- Source: /soft/amber8/dat/leap/cmd/leaprc.gaff
----- Source of /soft/amber8/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /soft/amber8/dat/leap/parm/gaff.dat
----- Source: /soft/amber8/dat/leap/cmd/leaprc.ff03
----- Source of /soft/amber8/dat/leap/cmd/leaprc.ff03 done
Log file: ./leap.log
Loading parameters: /soft/amber8/dat/leap/parm/parm99.dat
Loading parameters: /soft/amber8/dat/leap/parm/frcmod.ff03
Reading force field mod type file (frcmod)
Loading library: /soft/amber8/dat/leap/lib/ions94.lib
Loading library: /soft/amber8/dat/leap/lib/solvents.lib
Loading library: /soft/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /soft/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /soft/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /soft/amber8/dat/leap/lib/all_amino03.lib
Sourcing: ./teleap.in
Loading parameters: ./2OG.frcmod
Reading force field mod type file (frcmod)
Loading Prep file: ./2OG.in
Loading PDB file: ./1EA0_A.pdb
total atoms in file: 11190
Leap added 11222 missing atoms according to residue templates:
11222 H / lone pairs
8 Na+ ions required to neutralize.
Adding 8 counter ions to "1ea0" using 1A grid
Grid extends from solute vdw + 1.87 to 7.87
Resolution: 1.00 Angstrom.
grid build: 3 sec
(no solvent present)
Calculating grid charges
charges: 463 sec
Placed Na+ in 1ea0 at (91.65, 118.18, 96.59).
Placed Na+ in 1ea0 at (56.65, 180.18, 131.59).
Placed Na+ in 1ea0 at (27.65, 103.18, 84.59).
Placed Na+ in 1ea0 at (44.65, 172.18, 86.59).
Placed Na+ in 1ea0 at (14.65, 133.18, 104.59).
Placed Na+ in 1ea0 at (9.65, 95.18, 108.59).
Placed Na+ in 1ea0 at (34.65, 112.18, 70.59).
Placed Na+ in 1ea0 at (56.65, 120.18, 71.59).
Done adding ions.
Solute vdw bounding box: 99.030 95.487 96.959
Total bounding box for atom centers: 119.030 115.487 116.959
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 121.840 118.869 119.755 angstroms.
Volume: 1734411.844 A^3
Total mass 938519.388 amu, Density 0.899 g/cc
Added 43242 residues.
Checking Unit.
WARNING: There is a bond of 7.224966 angstroms between:
------- .R<THR 304>.A<C 13> and .R<THR 305>.A<N 1>
WARNING: There is a bond of 10.331638 angstroms between:
------- .R<VAL 1168>.A<C 15> and .R<ASP 1169>.A<N 1>
WARNING: There is a bond of 25.906360 angstroms between:
------- .R<GLY 1182>.A<C 6> and .R<GLY 1183>.A<N 1>
WARNING: There is a bond of 42.958738 angstroms between:
------- .R<LEU 1452>.A<C 18> and .R<2OG 1453>.A<O1 1>
WARNING: There is a bond of 4.303449 angstroms between:
------- .R<2OG 1453>.A<C4 11> and .R<2OG 1453>.A<O2 12>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - oh
Building angle parameters.
Could not find angle parameter: O - C - oh
Could not find angle parameter: C - oh - ho
Could not find angle parameter: C - oh - c
Could not find angle parameter: CT - C - oh
Building proper torsion parameters.
** No torsion terms for O-C-oh-ho
** No torsion terms for O-C-oh-c
** No torsion terms for CT-C-oh-ho
** No torsion terms for CT-C-oh-c
Building improper torsion parameters.
old PREP-specified impropers:
<2OG 1453>: C2 O5 C1 O1
<2OG 1453>: C5 C3 C4 O2
<2OG 1453>: C4 O4 C5 O3
total 4414 improper torsions applied
3 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
Quit
I do not understand what to do next. Will you please help me solve this problem.
Thanks u very much in advance.
Best Regards
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore
India
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Received on Wed Aug 13 2008 - 06:07:50 PDT
