Dear All,
I have repeated the procedure after the patches have been applied by
sysadmin and it seems to have solved the problem as expected/suggested by
Jason/David and others.
And the minimization job seems to be running OK.
I will keep a watch on all output files and messages therein and get back
to you for suggestion if there are errors.
Thank a lot again for your inputs and suggestions.
Cheers.
Vaibhav
ukmcdwlx005 136% tail P450_1W0E.inpcrd
46.7354253 46.6835314 -8.2104851 47.2794157 47.2965273 -8.7049896
46.1541098 47.2414893 -7.6937838 50.0583047 46.1431369 -8.8743529
49.2678591 46.1255507 -9.4139030 49.8216402 46.6819662 -8.1194493
44.8580311 44.3295081 -6.3476094 45.7271471 44.5035734 -6.7089459
44.3787063 45.1489498 -6.4700365 49.2305911 47.8162568 -6.7563249
48.8372857 47.2628766 -6.0815605 50.0472051 48.1273146 -6.3656732
51.5381770 52.3665228 -5.9664725 51.4378497 53.3159585 -6.0352634
51.3203312 52.0383467 -6.8388655 47.5118165 49.7373769 -7.7493221
48.3749626 49.3810573 -7.5389896 46.9383575 49.3987663 -7.0617816
96.5518122 96.5518122 96.5518122 109.4712190 109.4712190 109.4712190
On Tue, Apr 21, 2015 at 6:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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.
> >
>
> Your leap output shows that everything completed successfully. The
> problem is almost certainly the bug I mentioned in my previous email.
>
> You can use the command
>
> $AMBERHOME/update_amber --version
>
> to print out which updates have been applied. I strongly suspect that the
> answer is none. In which case, the admin will need to reconfigure and
> recompile Amber on the machine.
>
> Alternatively, you can download AmberTools 14 yourself and install it. But
> until Amber is updated, it might be hard to work around this bug. You
> could try to add another saveAmberParm command in order to *force* buffer
> flushing (I'm not sure if this will work or not). So something like this:
>
> 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 <http://p450.419.sg/> P450.477.FE
> solvateoct P450 TIP3PBOX 12
> charge P450
> addions P450 Cl- 0
> saveAmberParm
> P450 P450_1W0E_1.prmtop P450_1W0E_1.inpcrd
> saveAmberParm
> P450
> junk.prmtop junk.inpcrd
>
> Hopefully writing the junk.* files will flush the buffers for
> P450_1W0E_1.inpcrd. If not, you will have to wait for an update from the
> sysadmin.
>
>
>
>
> > 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.
> >
>
> It's not. Your input file is truncated, so it's missing information that
> sander and pmemd need for the simulation. The only way you can "fix" this
> is by providing an inpcrd file that is not truncated (memory amounts in
> sander are entirely unrelated to this).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 Thu Apr 23 2015 - 12:30:03 PDT
