Re: [AMBER] Need help in Targeted MD

From: Pallavi Mohanty <pallavipmohanty.gmail.com>
Date: Mon, 5 Jan 2015 17:31:47 +0530

Dear Dac,
This time i have changed the input tmd.in file i.e
TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
 &cntrl
      imin = 0, ntx = 5, nstlim = 5000, irest = 1,
      dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
      temp0 = 300.0,
      cut = 16.0,
      ntpr = 1, ntwx = 50, ntwr = 500,
      ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
      igb = 1, nscm = 0, nmropt = 1,
      ntr = 1, restraint_wt = 0.02,
      restraintmask = ":38-134",
      itgtmd = 1, tgtrmsd = 1.6, tgtmdfrc = 1.0,
      tgtrmsmask = "(:1-37)",
      /
 &wt
      TYPE='TGTRMSD', istep1=1, istep2=1000,
      value1 = 1.000, value2 = 0.0,
 /
 &wt
      TYPE='TGTRMSD', istep1=1000, istep2=0,
      value1 = 0.0, value2 = 0.0,
 /
 &wt
    type='END',
/
and the output file shows the following error :
FATAL: NATOM mismatch in constraint coord and topology files. Have attached
the out file too! Please help!


On Fri, Jan 2, 2015 at 6:36 PM, David A Case <case.biomaps.rutgers.edu>
wrote:

> On Fri, Jan 02, 2015, Pallavi Mohanty wrote:
> >
> > Dear Dac!
> > Tried using ntpr=1, Jobs stops saying "forrtl: severe (64): input
> > conversion error, unit -5, file Internal Formatted Read ".
> > And the out file states the same issue" INFO: Old style inpcrd file
> read"
> > Have attached the output file!
>
> I'm not sure what is triggering this message. Make sure that the input
> coordinate file doesn't have any "*" characters in it.
>
> Beyond that: the usual debugging: try turning off targetted options, to see
> if this *exact* set of input files can be made to run a short simulation.
> Basic idea is to simplify the input down until you can get it to work, then
> slowly work back towards what you want, so that you can better localize the
> source of the problem.
>
> ....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Regards,
Pallavi Mohanty



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


Received on Mon Jan 05 2015 - 04:30:03 PST
Custom Search