Dear Amber experts,
Recently, I'd like to utilize ff02pol.r1 to run a polarizable force field test.
I note the solution of zlzuo's question:
http://archive.ambermd.org/201306/0055.html
that under ff02pol.r1, I should
> loadamberparams frcmod.pol3
> set default IPOL 1
However, in my tests, both under Amber12 and Amber14, it seems LEaP didn't recognize the force field is polarizable (See the command lines below).
Does anyone know how to tell LEaP that I am using a polarizable FF?
I tried to modify the IPOL flag in PRMTOP file to 1, the minimization can run with pmemd.MPI, but I don't know if it could produce right results.
Thanks a lot for your attention and help!
Command lines and comments:
$ tleap -s -f leaprc.ff02pol.r1
-I: Adding /home/amber12-cuda5/dat/leap/prep to search path.
-I: Adding /home/amber12-cuda5/dat/leap/lib to search path.
-I: Adding /home/amber12-cuda5/dat/leap/parm to search path.
-I: Adding /home/amber12-cuda5/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff02pol.r1.
Welcome to LEaP!
Sourcing: /home/amber12-cuda5/dat/leap/cmd/leaprc.ff02pol.r1
Log file: ./leap.log
Loading parameters: /home/amber12-cuda5/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /home/amber12-cuda5/dat/leap/parm/frcmod.ff02pol.r1
Reading force field modification type file (frcmod)
Reading title:
DISABLE BACKBONE AND NO-HYDROGEN
Loading library: /home/amber12-cuda5/dat/leap/lib/all_nucleic02.lib
Loading library: /home/amber12-cuda5/dat/leap/lib/all_amino02.r1.lib
Loading library: /home/amber12-cuda5/dat/leap/lib/all_aminoct02.lib
Loading library: /home/amber12-cuda5/dat/leap/lib/all_aminont02.lib
Loading library: /home/amber12-cuda5/dat/leap/lib/ions94.lib
Loading library: /home/amber12-cuda5/dat/leap/lib/solvents.lib
> loadamberparams frcmod.pol3
Loading parameters: /home/amber12-cuda5/dat/leap/parm/frcmod.pol3
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for POL3 water
//Whether I load this paramter file or not, nothing changes.
> pdb = loadpdb 2L14.pdb
Loading PDB file: ./2L14.pdb
Added missing heavy atom: .R<CASP 61>.A<OXT 13>
total atoms in file: 391
Leap added 364 missing atoms according to residue templates:
1 Heavy
363 H / lone pairs
> addions pdb Na+ 0
10 Na+ ions required to neutralize.
Adding 10 counter ions to "pdb" using 1A grid
Grid extends from solute vdw + 4.15 to 10.15
Resolution: 1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in pdb at (13.48, -29.55, -4.80).
Placed Na+ in pdb at (24.48, -16.55, -1.80).
Placed Na+ in pdb at (17.48, -34.55, -17.80).
Placed Na+ in pdb at (33.48, 5.45, -3.80).
Placed Na+ in pdb at (27.48, -25.55, -8.80).
Placed Na+ in pdb at (10.48, -42.55, -22.80).
Placed Na+ in pdb at (1.48, -24.55, -5.80).
Placed Na+ in pdb at (34.48, -6.55, -2.80).
Placed Na+ in pdb at (12.48, -41.55, -13.80).
Placed Na+ in pdb at (13.48, -9.55, 3.20).
Done adding ions.
> saveamberparm pdb test.top test.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 144 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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
CASP 1
NPRO 1
)
(no restraints)
//If I don't solvate the protein, no warnings about IPOL flag reminded.
//Then I went on solvate the protein:
> solvateoct pdb TIP3PBOX 10
Scaling up box by a factor of 1.169184 to meet diagonal cut criterion
Solute vdw bounding box: 35.064 59.300 22.162
Total bounding box for atom centers: 82.684 82.684 82.684
(box expansion for 'iso' is 156.8%)
Solvent unit box: 18.774 18.774 18.774
Volume: 293018.499 A^3 (oct)
Total mass 156316.664 amu, Density 0.886 g/cc
Added 8355 residues.
//Actually, I've tried water models of TIP3PBOX, POL3BOX, PL3, but all things went the same.
> saveamberparm pdb test.top test.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 144 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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
CASP 1
NPRO 1
WAT 8355
)
(no restraints)
//Still, no warnings about IPOL reminded.
//BUT, if I set the IPOL to 1:
> loadamberparams frcmod.pol3
Loading parameters: /home/amber12-cuda5/dat/leap/parm/frcmod.pol3
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for POL3 water
> set default IPOL 1
> pdb = loadpdb 2L14.pdb
Loading PDB file: ./2L14.pdb
Added missing heavy atom: .R<CASP 61>.A<OXT 13>
total atoms in file: 391
Leap added 364 missing atoms according to residue templates:
1 Heavy
363 H / lone pairs
> addions pdb Na+ 0
10 Na+ ions required to neutralize.
Adding 10 counter ions to "pdb" using 1A grid
Grid extends from solute vdw + 4.15 to 10.15
Resolution: 1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 1 sec
Placed Na+ in pdb at (13.48, -29.55, -4.80).
Placed Na+ in pdb at (24.48, -16.55, -1.80).
Placed Na+ in pdb at (17.48, -34.55, -17.80).
Placed Na+ in pdb at (33.48, 5.45, -3.80).
Placed Na+ in pdb at (27.48, -25.55, -8.80).
Placed Na+ in pdb at (10.48, -42.55, -22.80).
Placed Na+ in pdb at (1.48, -24.55, -5.80).
Placed Na+ in pdb at (34.48, -6.55, -2.80).
Placed Na+ in pdb at (12.48, -41.55, -13.80).
Placed Na+ in pdb at (13.48, -9.55, 3.20).
Done adding ions.
> saveamberparm pdb test2.top test2.crd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 144 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Conflict: non-polarizable prmtop can not have IPOL > 0.
Please change IPOL in frcmod/parmxx.dat or set default IPOL.
//It seems that LEaP didn't recognize this as a polarizable FF
Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science,
Shanghai Jiaotong University,
800 Dongchuan RD, Shanghai, China.
Email: yw20055968.126.com
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Received on Thu Nov 06 2014 - 20:30:02 PST
