AMBER Archive (2009)

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

From: Yi Mao (maoyi0_at_gmail.com)
Date: Wed Jan 07 2009 - 08:46:05 CST

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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