AMBER Archive (2009)

Subject: Re: [AMBER] four prepin/frcmod files be read simultaneously by leap

From: Yi Mao (maoyi0_at_gmail.com)
Date: Wed Jan 07 2009 - 10:38:52 CST

Thanks very much for the information.

If the system only consisted the protein and any one of the ligands,
leap works just fine.

[ymao_at_research ~/2d1r]$ tleap -s -f leaprc.ff99
-I: Adding /usr/local/amber9//dat/leap/prep to search path.
-I: Adding /usr/local/amber9//dat/leap/lib to search path.
-I: Adding /usr/local/amber9//dat/leap/parm to search path.
-I: Adding /usr/local/amber9//dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff99.

Welcome to LEaP!
Sourcing: /usr/local/amber9//dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber9//dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading library: /usr/local/amber9//dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber9//dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber9//dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber9//dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber9//dat/leap/lib/ions94.lib
Loading library: /usr/local/amber9//dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /usr/local/amber9//dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber9//dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber9//dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> loadamberprep amp.prepin
Loading Prep file: ./amp.prepin
> loadamberparams amp.frcmod
Loading parameters: ./amp.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> 2d1s = loadPdb a.pdb
Loading PDB file: ./a.pdb
-- residue 28: duplicate [ CD] atoms (total 2)
-- residue 28: duplicate [ CG] atoms (total 2)
-- residue 28: duplicate [ NE2] atoms (total 2)
-- residue 28: duplicate [ OE1] atoms (total 2)
-- residue 354: duplicate [ CG2] atoms (total 2)
-- residue 354: duplicate [ OG1] atoms (total 2)
-- residue 233: duplicate [ CG1] atoms (total 2)
-- residue 233: duplicate [ CG2] atoms (total 2)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

  Added missing heavy atom: .R<LYS 15>.A<CD 11>
  Added missing heavy atom: .R<LYS 15>.A<CE 14>
  Added missing heavy atom: .R<LYS 15>.A<NZ 17>
  Added missing heavy atom: .R<GLU 22>.A<CD 11>
  Added missing heavy atom: .R<GLU 22>.A<OE1 12>
  Added missing heavy atom: .R<GLU 22>.A<OE2 13>
  Added missing heavy atom: .R<ARG 30>.A<NH1 17>
  Added missing heavy atom: .R<ARG 30>.A<NH2 20>
  Added missing heavy atom: .R<LYS 184>.A<NZ 17>
  Added missing heavy atom: .R<LYS 283>.A<NZ 17>
  Added missing heavy atom: .R<LEU 293>.A<CD1 10>
  Added missing heavy atom: .R<LEU 293>.A<CD2 14>
  Added missing heavy atom: .R<LYS 305>.A<CD 11>
  Added missing heavy atom: .R<LYS 305>.A<CE 14>
  Added missing heavy atom: .R<LYS 305>.A<NZ 17>
  Added missing heavy atom: .R<LYS 382>.A<CD 11>
  Added missing heavy atom: .R<LYS 382>.A<CE 14>
  Added missing heavy atom: .R<LYS 382>.A<NZ 17>
  Added missing heavy atom: .R<GLU 408>.A<CD 11>
  Added missing heavy atom: .R<GLU 408>.A<OE1 12>
  Added missing heavy atom: .R<GLU 408>.A<OE2 13>
  Added missing heavy atom: .R<LYS 411>.A<CD 11>
  Added missing heavy atom: .R<LYS 411>.A<CE 14>
  Added missing heavy atom: .R<LYS 411>.A<NZ 17>
  Added missing heavy atom: .R<GLU 412>.A<CD 11>
  Added missing heavy atom: .R<GLU 412>.A<OE1 12>
  Added missing heavy atom: .R<GLU 412>.A<OE2 13>
  Added missing heavy atom: .R<LEU 440>.A<CD1 10>
  Added missing heavy atom: .R<LEU 440>.A<CD2 14>
  Added missing heavy atom: .R<LYS 441>.A<CD 11>
  Added missing heavy atom: .R<LYS 441>.A<CE 14>
  Added missing heavy atom: .R<LYS 441>.A<NZ 17>
  Added missing heavy atom: .R<LYS 445>.A<CE 14>
  Added missing heavy atom: .R<LYS 445>.A<NZ 17>
  Added missing heavy atom: .R<SER 491>.A<OG 8>
  Added missing heavy atom: .R<LYS 493>.A<NZ 17>
  Added missing heavy atom: .R<GLU 539>.A<CG 8>
  Added missing heavy atom: .R<GLU 539>.A<CD 11>
  Added missing heavy atom: .R<GLU 539>.A<OE1 12>
  Added missing heavy atom: .R<GLU 539>.A<OE2 13>
  Added missing heavy atom: .R<LYS 542>.A<CD 11>
  Added missing heavy atom: .R<LYS 542>.A<CE 14>
  Added missing heavy atom: .R<LYS 542>.A<NZ 17>
  Added missing heavy atom: .R<LYS 543>.A<CG 8>
  Added missing heavy atom: .R<LYS 543>.A<CD 11>
  Added missing heavy atom: .R<LYS 543>.A<CE 14>
  Added missing heavy atom: .R<LYS 543>.A<NZ 17>
  Added missing heavy atom: .R<CVAL 545>.A<OXT 17>
  Added missing heavy atom: .R<CVAL 545>.A<CG1 7>
  Added missing heavy atom: .R<CVAL 545>.A<CG2 11>
  total atoms in file: 4132
  Leap added 4305 missing atoms according to residue templates:
       50 Heavy
       4255 H / lone pairs
> saveAmberParm 2d1s prmtop prmcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 0.999990 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <AMP 546>: C1' C4 N9 C8
 <AMP 546>: H8 N9 C8 N7
 <AMP 546>: C6 C4 C5 N7
 <AMP 546>: C5 N1 C6 N6
 <AMP 546>: C6 HN62 N6 HN61
 <AMP 546>: H2 N1 C2 N3
 <AMP 546>: C5 N9 C4 N3
 total 1595 improper torsions applied
 7 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CVAL 1
        NASP 1
  )
 (no restraints)
> quit
        Quit

a.pdb is the orginal pdb file minus one ligand. Although there are the
same warnings regarding some protein residues, leap is successful and
the prmtop and prmcrd files are generated.

So my question is still why adding one more ligand won't work with leap?

Yi

On Wed, Jan 7, 2009 at 11:05 AM, <rpaduri_at_chem.wayne.edu> wrote:
> Hi Yi,
> Theoretically speaking you can add as many "prepin" and "frcmod" files as you
> like to leap. Based on your output, I would first look at residues 28, 354, and
> 233. I think you are also having some issue with the atomtypes. Which atomtypes
> did you use in your prepin file. Since you are loading the "gaff", you may want
> to use the gaff atomtypes and that may help you with the atomtype issues. I hope
> this helps.
> Sincerely
> Raviprasad Aduri
>
> Quoting Yi Mao <maoyi0_at_gmail.com>:
>
>> I have a complex consisting of a protein and two organic molecules
>> (named AMP and OLU respectively). I used antechamber to generate four
>> files: amp.prepin/amp.frcmod and olu.prepin/olu.frcmod.
>>
>> However, I am having a difficulty to load all of these four files to
>> leap (I am using AMBER 9) at the same time.
>>
>> Welcome to LEaP!
>> Sourcing: /usr/local/amber9//dat/leap/cmd/leaprc.ff99
>> Log file: ./leap.log
>> Loading parameters: /usr/local/amber9//dat/leap/parm/parm99.dat
>> Reading title:
>> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
>> incl.02/04/99
>> Loading library: /usr/local/amber9//dat/leap/lib/all_nucleic94.lib
>> Loading library: /usr/local/amber9//dat/leap/lib/all_amino94.lib
>> Loading library: /usr/local/amber9//dat/leap/lib/all_aminoct94.lib
>> Loading library: /usr/local/amber9//dat/leap/lib/all_aminont94.lib
>> Loading library: /usr/local/amber9//dat/leap/lib/ions94.lib
>> Loading library: /usr/local/amber9//dat/leap/lib/solvents.lib
>> > source leaprc.gaff
>> ----- Source: /usr/local/amber9//dat/leap/cmd/leaprc.gaff
>> ----- Source of /usr/local/amber9//dat/leap/cmd/leaprc.gaff done
>> Log file: ./leap.log
>> Loading parameters: /usr/local/amber9//dat/leap/parm/gaff.dat
>> Reading title:
>> AMBER General Force Field for organic mol., add. info. at the end (June,
>> 2003)
>> > loadamberprep amp.prepin
>> Loading Prep file: ./amp.prepin
>> > loadamberprep olu.prepin
>> Loading Prep file: ./olu.prepin
>> > loadamberparams amp.frcmod
>> Loading parameters: ./amp.frcmod
>> Reading force field modification type file (frcmod)
>> Reading title:
>> remark goes here
>> > loadamberparams olu.frcmod
>> Loading parameters: ./olu.frcmod
>> Reading force field modification type file (frcmod)
>> Reading title:
>> remark goes here
>> > 2d1s = loadPdb mod.pdb
>> Loading PDB file: ./mod.pdb
>> -- residue 28: duplicate [ CD] atoms (total 2)
>> -- residue 28: duplicate [ CG] atoms (total 2)
>> -- residue 28: duplicate [ NE2] atoms (total 2)
>> -- residue 28: duplicate [ OE1] atoms (total 2)
>> -- residue 354: duplicate [ CG2] atoms (total 2)
>> -- residue 354: duplicate [ OG1] atoms (total 2)
>> -- residue 233: duplicate [ CG1] atoms (total 2)
>> -- residue 233: duplicate [ CG2] atoms (total 2)
>>
>> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
>> (same-name atoms are reduced to a single atom)
>>
>> Added missing heavy atom: .R<LYS 15>.A<CD 11>
>> Added missing heavy atom: .R<LYS 15>.A<CE 14>
>> Added missing heavy atom: .R<LYS 15>.A<NZ 17>
>> Added missing heavy atom: .R<GLU 22>.A<CD 11>
>> Added missing heavy atom: .R<GLU 22>.A<OE1 12>
>> Added missing heavy atom: .R<GLU 22>.A<OE2 13>
>> Added missing heavy atom: .R<ARG 30>.A<NH1 17>
>> Added missing heavy atom: .R<ARG 30>.A<NH2 20>
>> Added missing heavy atom: .R<LYS 184>.A<NZ 17>
>> Added missing heavy atom: .R<LYS 283>.A<NZ 17>
>> Added missing heavy atom: .R<LEU 293>.A<CD1 10>
>> Added missing heavy atom: .R<LEU 293>.A<CD2 14>
>> Added missing heavy atom: .R<LYS 305>.A<CD 11>
>> Added missing heavy atom: .R<LYS 305>.A<CE 14>
>> Added missing heavy atom: .R<LYS 305>.A<NZ 17>
>> Added missing heavy atom: .R<LYS 382>.A<CD 11>
>> Added missing heavy atom: .R<LYS 382>.A<CE 14>
>> Added missing heavy atom: .R<LYS 382>.A<NZ 17>
>> Added missing heavy atom: .R<GLU 408>.A<CD 11>
>> Added missing heavy atom: .R<GLU 408>.A<OE1 12>
>> Added missing heavy atom: .R<GLU 408>.A<OE2 13>
>> Added missing heavy atom: .R<LYS 411>.A<CD 11>
>> Added missing heavy atom: .R<LYS 411>.A<CE 14>
>> Added missing heavy atom: .R<LYS 411>.A<NZ 17>
>> Added missing heavy atom: .R<GLU 412>.A<CD 11>
>> Added missing heavy atom: .R<GLU 412>.A<OE1 12>
>> Added missing heavy atom: .R<GLU 412>.A<OE2 13>
>> Added missing heavy atom: .R<LEU 440>.A<CD1 10>
>> Added missing heavy atom: .R<LEU 440>.A<CD2 14>
>> Added missing heavy atom: .R<LYS 441>.A<CD 11>
>> Added missing heavy atom: .R<LYS 441>.A<CE 14>
>> Added missing heavy atom: .R<LYS 441>.A<NZ 17>
>> Added missing heavy atom: .R<LYS 445>.A<CE 14>
>> Added missing heavy atom: .R<LYS 445>.A<NZ 17>
>> Added missing heavy atom: .R<SER 491>.A<OG 8>
>> Added missing heavy atom: .R<LYS 493>.A<NZ 17>
>> Added missing heavy atom: .R<GLU 539>.A<CG 8>
>> Added missing heavy atom: .R<GLU 539>.A<CD 11>
>> Added missing heavy atom: .R<GLU 539>.A<OE1 12>
>> Added missing heavy atom: .R<GLU 539>.A<OE2 13>
>> Added missing heavy atom: .R<LYS 542>.A<CD 11>
>> Added missing heavy atom: .R<LYS 542>.A<CE 14>
>> Added missing heavy atom: .R<LYS 542>.A<NZ 17>
>> Added missing heavy atom: .R<LYS 543>.A<CG 8>
>> Added missing heavy atom: .R<LYS 543>.A<CD 11>
>> Added missing heavy atom: .R<LYS 543>.A<CE 14>
>> Added missing heavy atom: .R<LYS 543>.A<NZ 17>
>> Added missing heavy atom: .R<CVAL 545>.A<OXT 17>
>> Added missing heavy atom: .R<CVAL 545>.A<CG1 7>
>> Added missing heavy atom: .R<CVAL 545>.A<CG2 11>
>> total atoms in file: 4148
>> Leap added 4311 missing atoms according to residue templates:
>> 50 Heavy
>> 4261 H / lone pairs
>> > saveAmberParm 2d1s prmtop prmcrd
>> Checking Unit.
>> WARNING: There is a bond of 6.113040 angstroms between:
>> ------- .R<AMP 546>.A<C4 35> and .R<OLU 547>.A<N3' 1>
>> WARNING: The unperturbed charge of the unit: 0.999990 is not zero.
>>
>> -- ignoring the warnings.
>>
>> Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Building angle parameters.
>> Could not find angle parameter: ca - ne - c
>> Could not find angle parameter: ca - ne - cf
>> Could not find angle parameter: nb - ca - ne
>> Could not find angle parameter: na - ca - ne
>> Building proper torsion parameters.
>> ** No torsion terms for ca-ne-cf-ss
>> ** No torsion terms for ca-ne-cf-cd
>> Building improper torsion parameters.
>> old PREP-specified impropers:
>> <AMP 546>: C1' C4 N9 C8
>> <AMP 546>: H8 N9 C8 N7
>> <AMP 546>: C6 C4 C5 N7
>> <AMP 546>: C5 N1 C6 N6
>> <AMP 546>: C6 HN62 N6 HN61
>> <AMP 546>: H2 N1 C2 N3
>> <AMP 546>: C5 N9 C4 N3
>> <OLU 547>: C5' N3' C4' O6'
>> <OLU 547>: C2 N3' C2' S1'
>> <OLU 547>: C2' N3 C2 S1
>> <OLU 547>: C6 C4 C5 S1
>> <OLU 547>: C5 C7 C6 H6
>> <OLU 547>: C6 C8 C7 O7
>> <OLU 547>: C7 C9 C8 H8
>> <OLU 547>: C8 C4 C9 H9
>> <OLU 547>: C5 C9 C4 N3
>> total 1604 improper torsions applied
>> 16 improper torsions in old prep form
>> Building H-Bond parameters.
>> Parameter file was not saved.
>>
>> It looks like the loadamberparams command didn't take effect. I have
>> tried to switch the order of the commands loadamberprep and
>> loadamberparams. The outcome is always that only two files generated
>> by antechamber can be processed by leap. I also tried to use leap on
>> the system of the protein and one ligand (AMP or OLU), and both worked
>> just fine.
>>
>> I notice it is possible to load two prepin files and two frcmod files in the
>> following link
>> http://www.ccl.net/chemistry/resources/messages/2007/08/10.006-dir/index.html
>>
>> So what are the things I might have missed?
>>
>> Thanks in advance
>>
>>
>> Yi Mao
>> Department of Mathematics
>> Michigan State University
>>
>> _______________________________________________
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>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>
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