Dear Prof. Case and Amber users,
Thanks for the suggestions. How can I use the ff14SB without access to
Amber14?
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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Received on Tue Apr 07 2015 - 06:00:02 PDT
