hi alessandro
Thank you so much. The problem was with not having "TER" between ligand and
protein in the pdb file.
Now the .top files are generated.
best regards
moitrayee
> Seems that your pdb file has some missing residues. Did you try to use
> "TER" in the 'gaps'?
> Do you have a "TER" between your ligand and your protein in the pdb file?
>
> HTH,
>
>
> -alessandro
>
> On Tue, Aug 12, 2008 at 4:20 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
>> 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
