Hi
It's 15049 residues not atoms, sorry for the wrong term.
On Tuesday 21 April 2015, Kenneth Huang <kennethneltharion.gmail.com> wrote:
> >
> > Just wondering is there a way to specify increased memory to sander and
> how
> > much in this case may be required (15049 atoms after adding waters), if
> > that's one of the issue beside the updates.
>
>
> I could be wrong on this, but I don't think there is a way to specify how
> much memory sander uses. That said, 15049 atoms isn't all that large of a
> system with water, especially not enough that it'd be causing it to crash.
> Obviously, it depends on your machine specifications, but I think it's well
> within a reasonable range, so I'd peg it as one the less likely candidates
> for the problem.
>
> If you wanted to check, I think one of the tutorials (MMPBSA?) has a
> similarly sized system that you could try try minimizing to verify.
>
> Best,
>
> Kenneth
>
> On Tue, Apr 21, 2015 at 12:16 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> <javascript:;>>
> wrote:
>
> > Hi all,
> > Thanks everybody for your vital inputs and explanation on the possible
> bug.
> > The detailed output from the tleap including saveambeparm command is
> given
> > at the end here (sorry for not including the whole thing earlier).
> > I will check with our system admin for the updates.
> > Just wondering is there a way to specify increased memory to sander and
> how
> > much in this case may be required (15049 atoms after adding waters), if
> > that's one of the issue beside the updates.
> > Thanks all.
> > Cheers.
> > Vaibhav
> >
> >
> > ukmcdwlx005 448% tleap -s -f leap.in
> > -I: Adding /apps/ambertools/amber14/rhel6-x64/dat/leap/prep to search
> path.
> > -I: Adding /apps/ambertools/amber14/rhel6-x64/dat/leap/lib to search
> path.
> > -I: Adding /apps/ambertools/amber14/rhel6-x64/dat/leap/parm to search
> path.
> > -I: Adding /apps/ambertools/amber14/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/amber14/rhel6-x64/dat/leap/cmd/leaprc.ff14SB
> > ----- Source of
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/cmd/leaprc.ff14SB done
> > Log file: ./leap.log
> > Loading parameters:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/parm/parm10.dat
> > Reading title:
> > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > Loading parameters:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/parm/frcmod.ff14SB
> > Reading force field modification type file (frcmod)
> > Reading title:
> > ff14SB protein backbone and sidechain parameters
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/amino12.lib
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/aminoct12.lib
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/aminont12.lib
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/nucleic12.lib
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/atomic_ions.lib
> > Loading library:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/lib/solvents.lib
> > ----- Source: /apps/ambertools/amber14/rhel6-x64/dat/leap/cmd/leaprc.gaff
> > ----- Source of
> /apps/ambertools/amber14/rhel6-x64/dat/leap/cmd/leaprc.gaff
> > done
> > Log file: ./leap.log
> > Loading parameters:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/parm/gaff.dat
> > Reading title:
> > AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
> > Loading Mol2 file: ./CYS_HS.mol2
> > Reading MOLECULE named CYP-IC6
> > UNIT name: CYP-IC6
> > Head atom: .R<CYP 1>.A<N 1>
> > Tail atom: .R<CYP 1>.A<C 9>
> > Contents:
> > R<CYP 1>
> > 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
> > Loading parameters:
> > /apps/ambertools/amber14/rhel6-x64/dat/leap/parm/frcmod.ionsjc_tip3p
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> > JPCB (2008)
> > Loading PDB file: ./1W0E_P450_leap.pdb
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-NB-FE-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-NA-FE-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-ND-FE-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > +---Tried to superimpose torsions for: *-NC-FE-*
> > +--- With Sp2 - Sp0
> > +--- Sp0 probably means a new atom type is involved
> > +--- which needs to be added via addAtomTypes
> > total atoms in file: 7800
> > Scaling up box by a factor of 1.282512 to meet diagonal cut criterion
> > Solute vdw bounding box: 79.806 73.249 48.124
> > Total bounding box for atom centers: 105.456 105.456 105.456
> > (box expansion for 'iso' is 52.4%)
> > Solvent unit box: 18.774 18.774 18.774
> > Volume: 603225.282 A^3 (oct)
> > Total mass 326127.024 amu, Density 0.898 g/cc
> > Added 15049 residues.
> > Total unperturbed charge: 2.000000
> > Total perturbed charge: 2.000000
> > 2 Cl- ions required to neutralize.
> > Adding 2 counter ions to "P450" using 1A grid
> > Grid extends from solute vdw + 2.51 to 8.51
> > 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 (14.17, 17.69, -12.61).
> > (Replacing solvent molecule)
> > Placed Cl- in P450 at (10.13, 18.65, 13.67).
> >
> > Done adding ions.
> > > saveamberparm P450 P450_1W0E_1.prmtop P450_1W0E_1.inpcrd
> > Checking Unit.
> > 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.
> > 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
> >
> > CTHR 1
> > CYP 1
> > HEM 1
> > WAT 15047
> > )
> > (no restraints)
> > >
> >
> >
> > On Tue, Apr 21, 2015 at 4:07 PM, David A Case <case.biomaps.rutgers.edu
> <javascript:;>>
> > wrote:
> >
> > > On Tue, Apr 21, 2015, Vaibhav Dixit wrote:
> > > >
> > > > kmcdwlx005 462% tail P450_test.inpcrd
> > > > 12.9410318 24.7763059 28.5292431 6.0666578 11.2373217
> > 31.8421776
> > > > 5.7263398 10.4381030 32.2442456 5.3605584 11.5374928
> > 31.2698610
> > > > 6.7183050 8.3222530 30.2949099 7.5409119 7.8483008
> > 30.1727990
> > > > 6.9621113 9.1013013 30.7947786 4.2421629 15.0141650
> > 28.1041078
> > > > 4.0966209 15.3281953 28.9965360 3.7646832 15.6326551
> > 27.5511977
> > > > 6.1018012 12.0044198 28.1521968 6.0879580 11.1085292
> > 27.8154266
> > > > 6.8190440 12.0114862 28.7860254 7.9544142 12.4381539
> > 30.1975095
> > > > 7.6961920 13.3598609 30.1959426 7.4229183 12.0411973
> > 30.8875559
> > > > 12.8990331 25.5432326 22.9765180 13.0727209 24.9778748
> > 22.2239033
> > > > 13.3919222 26.3433221 22.7944670 8.3746098 8.5713
> > >
> > > This file looks truncated, as thought the the LEaP program did not
> > > correctly
> > > complete, or there were a disk error, or something like that.
> > >
> > > >
> > > > My current leap.in
> > > > ukmcdwlx005 463% more leap.in
> > > > source leaprc.ff14SB
> > > > source leaprc.gaff
> > > > CYP = loadmol2 CYS_HS.mol2
> > > > set CYP head CYP.1.N
> > > > set CYP tail CYP.1.C
> > > > desc CYP
> > > > HEM = loadmol2 HEM_pentacoordinateHS.mol2
> > > > loadamberparams HEM_HS.frcmod
> > > > loadamberparams frcmod.ionsjc_tip3p
> > > > P450 = loadpdb 1W0E_P450_leap.pdb
> > > > bond P450.419.SG P450.477.FE
> > > > solvateoct P450 TIP3PBOX 12
> > > > charge P450
> > > > addions P450 Cl- 0
> > > >
> > >
> > > I'll assume(?) you had a saveAmberParm command somewhere, and decided
> not
> > > to let us see it. Check the leap.log file for errors. Try re-running
> > the
> > > script. Now that you know to run "tail" on the inpcrd file, you can
> > start
> > > to debug the problem. Check both the output that comes to stdout, and
> > the
> > > info in leap.log to try to find out what is going on.
> > >
> > > ...good luck....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > 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 <javascript:;>
> > Moblie Number: +44-7448233157, +91-7709129400.
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > Please consider the environment before printing this e-mail
> > _______________________________________________
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> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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--
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
Please consider the environment before printing this e-mail
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Received on Tue Apr 21 2015 - 10:30:03 PDT
