AMBER Archive (2008)

Subject: Re: AMBER: empty frcmod file but missing parameters

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Tue Aug 12 2008 - 17:02:01 CDT

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_at_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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