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
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Received on Tue Apr 21 2015 - 09:30:09 PDT
