AMBER Archive (2009)

Subject: Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule.

From: Soni Mufaddal Saifee (muffisoni_at_gmail.com)
Date: Tue Apr 07 2009 - 23:19:25 CDT

Dear Carlos,

Thanks for your help.. I made the change and the system is running perfectly
fine now..
Thanks again..

Mufaddal

On Mon, Apr 6, 2009 at 3:37 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> this has been discussed before, you might find more info searching the
> archives.
> in short, you need to use iwrap=1 for long runs. you also might need to add
> the box size to the end of your inpcrd (I think ptraj may not do it
> automatically). it is in the trajectory file right after the coordinates,
> you can see it by looking at that frame with a file editor (or using the
> unix tail command if it is the last frame in the file). if it is constant
> volume, then you can use the box size from any of the other equilibrated
> restarts since it won't change. make sure you put the box coordinates in
> the
> same format as other restart files, don't just copy and paste from the
> trajectory file since the formats differ.
>
>
> On Mon, Apr 6, 2009 at 5:07 AM, Soni Mufaddal Saifee <muffisoni_at_gmail.com
> >wrote:
>
> > Dear Amber users,
> >
> > I have been carrying out a simulation of a protein-ligand explicit water
> MD
> > simulation using the ff99SB force-field. After completing about 50ns of
> the
> > run, suddenly the output .rst file of my run had "************" signs
> > instead of the x-co-ordinates of the 3 atoms of a certain water molecule.
> > Something like this:
> >
> > 362.5312633 267.2621357-103.1379393-153.5429259-199.6611347-123.3177335
> > -153.8078616-198.8575496-122.8701936-152.7184258-199.9079292-122.8987778
> > 44.5051355-207.9254210 59.0354869 43.9546665-207.7149791 59.7897613
> > 45.4000580-207.7895160 59.3467348************ 74.1218262-104.0510373
> > ************ 73.6745789-103.2063682************ 73.5659402-104.5814460
> > -365.9189866 447.8853764 -30.3888650-365.5955834 447.5974812 -31.2425385
> > -365.7685621 447.1372462 -29.8110194-104.6516299 88.9232533 -40.5432262
> > -104.7796026 89.8573816 -40.7083297-104.1181933 88.6209863 -41.2782853
> > 245.4157167 244.9111976 456.5944703 244.8351246 245.6404763 456.3769909
> > 245.4239023 244.3682718 455.8061833 519.1683584 -99.5645316 -49.2072520
> >
> > Cause of this, I could not restart my run and hence had to generate yet
> > another .rst file of an earlier frame from the same run using the ptraj
> > module. I then renamed the new .rst file as a .crd file and changed the
> ntx
> > = 7, irest = 1, to ntx = 1, irest = 0, in the .in file for the new run.
> >
> > when I submit this particular run my job gets stuck at a particular
> > position
> > and does not move further.
> >
> > File Assignments:
> > | MDIN: pr55.in
> > | MDOUT: pr55.out
> > |INPCRD: pr544.crd
> > | PARM: top_leap.top
> > |RESTRT: pr55.rst
> > | REFC: pr544.crd
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: pr55.crd
> > |MDINFO: pr55.info
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > rm to 300K quickly,
> > &cntrl
> > imin = 0, ntx = 1, irest = 0,
> > ntpr = 100, ntwx = 500, ntwe = 0,
> > ntc = 2, ntf = 2,
> > nstlim = 1000000, dt =0.002,
> > tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> > ntb = 2, ntp = 1, taup = 0.2, pres0 =1.0,ntr=0
> > &end
> > END
> >
> >
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> >
> > | Flags: MPI
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> >
> > I do not kno how to move further ahead with it. If any one has ever faced
> > this problem, it would be great if you could help me out.
> > Also if any one knows, why the software generated the "************"
> signs
> > in my .rst file in the first place, please do let me kno.
> >
> > thanks in advance..
> >
> > Mufaddal
> >
> >
> > --
> > Soni Mufaddal Saifee
> > Fourth (Senior) Year B.Tech
> > Dept. of Biotechnology
> > IIT Madras.
> >
> >
> > "The will of God will never take you where the grace of God will not
> > protect
> > you."
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> 

-- 
Soni Mufaddal Saifee
Fourth (Senior) Year B.Tech
Dept. of Biotechnology
IIT Madras.

"The will of God will never take you where the grace of God will not protect
you."
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