AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Apr 06 2009 - 05:07:09 CDT

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
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber