AMBER Archive (2008)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue Aug 12 2008 - 17:10:03 CDT

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_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

> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu