>
> 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>
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>
> 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
> > 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
>
> Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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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Received on Tue Apr 21 2015 - 10:00:04 PDT
