On Tue, Apr 7, 2015 at 6:54 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear Prof. Case and Amber users,
> Thanks for the suggestions. How can I use the ff14SB without access to
> Amber14?
With the exception of PMEMD, everything in Amber (including force
fields) is freely available via AmberTools:
http://ambermd.org/AmberTools14-get.html
-Dan
>
> Based on these suggestions I have tried to use a short fix as follows:
>
> I have deleted these atoms with error message from the pdb (new pdb
> attached) and removed the atom connection information with the hope that
> leap will fix them automatically.
> Then reran the same set of commands from the leap.in file and it has saved
> the param and inpcrd files (attached), but the partial charge is still
> there.
> Is it likely due to cause problems while running the MD simulation?
> I haven't connected the S-Fe bonds in the pdb, thus it should have given
> some error message related to that, but why there is no such error?
> check command is returning only one error and four warnings.
> And finally are these prmtop and inpcrd likely to be sensible?
>
> Thanks a lot.
> Cheers.
> Vaibhav
>
> Leap input:
> source leaprc.ff99SB
> source leaprc.gaff
> HEM = loadmol2 HEM_pentacoordinateHS.mol2
> loadamberparams HEM_HS.frcmod
> P450 = loadpdb 1W0E_prepared1.pdb
> solvateoct P450 TIP3PBOX 12
> charge P450
> addions P450 Cl- 0
>
> Leap output:
> ukmcdwlx005 123% tleap -s -f leap.in
> -I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/prep to search path.
> -I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/lib to search path.
> -I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/parm to search path.
> -I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leap.in.
>
> Welcome to LEaP!
> Sourcing: ./leap.in
> ----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB
> ----- Source of
> /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB done
> Log file: ./leap.log
> Loading parameters:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_nucleic94.lib
> Loading library:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_amino94.lib
> Loading library:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminont94.lib
> Loading library: /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/ions94.lib
> Loading library:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/solvents.lib
> ----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
> ----- Source of /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
> done
> Log file: ./leap.log
> Loading parameters:
> /apps/ambertools/amber12/rhel6-x64/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> add. info. at the end
> Loading Mol2 file: ./HEM_pentacoordinateHS.mol2
> Reading MOLECULE named HEM-IC6
> Loading parameters: ./HEM_HS.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Unknown keyword:
> in parameter file. Perhaps a format error?
> Loading PDB file: ./1W0E_prepared1.pdb
> Added missing heavy atom: .R<ACE 24>.A<C 5>
> Added missing heavy atom: .R<ACE 24>.A<O 6> total atoms in file: 7773
> Leap added 27 missing atoms according to residue templates:
> 9 Heavy
> 18 H / lone pairs
> Scaling up box by a factor of 1.278441 to meet diagonal cut criterion
> Solute vdw bounding box: 48.125 79.806 73.250
> Total bounding box for atom centers: 110.489 110.489 110.489
> (box expansion for 'iso' is 49.0%)
> Solvent unit box: 18.774 18.774 18.774
> Volume: 692888.074 A^3 (oct)
> Total mass 377886.992 amu, Density 0.906 g/cc
> Added 17922 residues.
> Total unperturbed charge: 2.402400
> Total perturbed charge: 2.402400
> 2 Cl- ions required to neutralize.
> Adding 2 counter ions to "P450" using 1A grid
> Grid extends from solute vdw + 2.47 to 8.47
> Resolution: 1.00 Angstrom.
> grid build: 0 sec
> Solvent present: replacing closest with ion
> when steric overlaps occur
> Calculating grid charges
> charges: 15 sec
> (Replacing solvent molecule)
> Placed Cl- in P450 at (-3.41, 13.29, -21.14).
> (Replacing solvent molecule)
> Placed Cl- in P450 at (-21.91, 3.86, -12.60).
>
> Done adding ions.
>> saveamberparm P450 P450_1W0E.prmtop P450_1W0E.inpcrd
> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.402400 is not integral.
> WARNING: The unperturbed charge of the unit: 0.402400 is not zero.
>
> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1497 improper torsions applied
> 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
>
> ACE 1
> CTHR 1
> HEM 1
> WAT 17920
> )
> (no restraints)
>> check P450
> Checking 'P450'....
> ERROR: The unperturbed charge of the unit: 0.402400 is not integral.
> WARNING: The unperturbed charge of the unit: 0.402400 is not zero.
> Warning: Close contact of 1.478811 angstroms between .R<ACE 24>.A<C 5> and
> .R<TYR 25>.A<H 2>
> Warning: Close contact of 1.174515 angstroms between .R<HIE 402>.A<HE2 13>
> and .R<THR 433>.A<H 2>
> Warning: Close contact of 1.379398 angstroms between .R<GLY 498>.A<O 7> and
> .R<CTHR 499>.A<HG21 8>
> Checking parameters for unit 'P450'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 4
>>
>
> On Tue, Apr 7, 2015 at 1:10 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Tue, Apr 07, 2015, Vaibhav Dixit wrote:
>>
>> > I have prepared the PDB in Schrodinger package (attached) ....
>>
>> > Loading PDB file: ./1W0E_prepared.pdb
>> > Created a new atom named: H within residue: .R<ACE 24>
>>
>> This means that you have a residue named "H" in your pdb file, which is
>> not in
>> the Amber residue (from its library) named ACE. Atom names in the PDB file
>> and in the residue libraries must match exactly. You will need to edit
>> your PDB file fix this. Same for the other "new atom" commands listed
>> below:
>>
>> > Created a new atom named: H1 within residue: .R<TYR 25>
>> > Created a new atom named: HE2 within residue: .R<GLU 97>
>> > Created a new atom named: HD2 within residue: .R<ASP 270>
>> > Created a new atom named: HE2 within residue: .R<GLU 320>
>> > Created a new atom named: HD1 within residue: .R<HIE 324>
>> > Created a new atom named: HD1 within residue: .R<HIE 402>
>> > Created a new atom named: H1 within residue: .R<CTHR 499>
>> > Created a new atom named: H2 within residue: .R<CTHR 499>
>>
>> For the histidines, note that the default in Amber is for histidines to be
>> of
>> type HIE. But your pdb file has hydrogens that make this either HID or
>> HIP.
>> Also, it looks like the preparation scheme you used has neutral
>> carboxylates
>> at residues 97, 270 and 320. You will have to decide if these are what you
>> want or not. Protonated residues in Amber are called ASH and GLH.
>>
>> p.s.: We recommend that you use ff14SB, not ff99SB.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> With Regards.
>
> Dr. Vaibhav A. Dixit,
> Postdoctoral Research Scientist,
> Etherow F40/6,
> AstraZeneca,
> Charter Way,
> Silk Road Business Park,
> Macclesfield,
> Cheshire,
> England,
> SK10 2NX
> Ext. No. 20278
> Email: Vaibhav.Dixit.astrazeneca.com
> Moblie Number: +44-7448233157, +91-7709129400.
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Tue Apr 07 2015 - 07:30:04 PDT
