On Mon, Apr 25, 2011 at 10:35 AM, Vaibhav Jain <xtreme.vaibhav.gmail.com>wrote:
> hii Jason,
>
> Thanks for your suggestion.
>
> I used the following input for the production phase.
>
> molecular dynamics production run
> &cntrl
> imin=0, ntx=5,irest=1,
> ntb=1,cut=8.0,
> ntp=0,
> ntc=2,
> ntf=2,
> ntt=3, temp0=310.0, gamma_ln=1.0,
> nstlim=200000, dt=0.002,
> iwrap=1,ioutfm=0,
> ntpr=1000, ntwr=50000, ntave=1000, ntwx=1000,
> ig=-1,
> /
>
>
> nw, u can see clearly I have already used iwrap=1 and ioutfm=0, but still
> error occurs that I have previously mentioned.
>
> So wt to do in this situation???
>
Well, something has been corrupted. Do you have *****s in your mdcrd file?
>
>
>
> On Mon, Apr 25, 2011 at 9:26 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Apr 25, 2011 at 8:16 AM, Vaibhav Jain <xtreme.vaibhav.gmail.com
> > >wrote:
> >
> > > Dear AMBER users,
> > >
> > > While running extract_coords.mmpbsa script file for extracting the
> > > trajectories from mdcrd file in AMBER10, I am getting following error.
> > >
> > >
> > > *At line 437 of file _make_crd_hg.f
> > > Fortran runtime error: Bad value during floating point read*
> > >
> >
> > Look at your trajectory file and search for *******. My bet is that your
> > trajectory file was corrupted because iwrap was set to 0 (or not set at
> > all)
> > in your input file, so diffusion took your particles outside the range
> > allowable by the fixed format ASCII trajectory file. Unfortunately this
> > means that your trajectory is largely useless.
> >
> > May I suggest that in the future you use the variable ioutfm=1 in your
> > sander/pmemd input files to print out NetCDF trajectories, and use
> > MMPBSA.py
> > (which is part of AmberTools 1.5), since NetCDF doesn't suffer from the
> > field-width restrictions of the ASCII file (and it's also faster to
> write,
> > load, etc.). Look on the Amber mailing list archives for "iwrap" and
> > "netcdf" and you'll see lengthy discussions on this topic.
> >
> > HTH,
> > Jason
> >
> >
> > >
> > > This is my input file.....
> > >
> > > .GENERAL
> > > PREFIX snapshot
> > > PATH ./
> > > COMPLEX 1
> > > RECEPTOR 1
> > > LIGAND 1
> > > COMPT ./comp.prmtop
> > > RECPT ./protein.prmtop
> > > LIGPT ./ligand.prmtop
> > > GC 1
> > > AS 0
> > > DC 0
> > > MM 0
> > > GB 0
> > > PB 0
> > > MS 0
> > > NM 0
> > > .MAKECRD
> > > BOX YES
> > > NTOTAL 84332
> > > NSTART 1
> > > NSTOP 1800
> > > NFREQ 20
> > > NUMBER_LIG_GROUPS 1
> > > LSTART 6061
> > > LSTOP 6101
> > > NUMBER_REC_GROUPS 2
> > > RSTART 1
> > > RSTOP 6060
> > > RSTART 6102
> > > RSTOP 6102
> > > .TRAJECTORY
> > > TRAJECTORY ./prod.mdcrd
> > > #TRAJECTORY ./prod2.mdcrd
> > > #TRAJECTORY ./prod3.mdcrd
> > > #TRAJECTORY ./prod4.mdcrd
> > > .PROGRAMS
> > >
> > >
> > > In my input file atoms 1-6060 corresponds to protein, 6061-6101
> > corresponds
> > > to ligand and 6102-6102 corresponds to magnesium ion.
> > >
> > > Please help me to get rid from this error.
> > >
> > >
> > > Thanks in advance.
> > >
> > >
> > >
> > > --
> > > *Warm Regards *
> > >
> > > Vaibhav Jain
> > > Ph.D. Scholar
> > > Department of Pharmacoinformatics
> > > NIPER, Mohali (Punjab), India
> > > MOb no. +919988412195
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> *Warm Regards *
>
> Vaibhav Jain
> Ph.D. Scholar
> Centre For Pharmacoinformatics
> NIPER, Mohali (Punjab)
> MOb no. +919988412195
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 25 2011 - 11:30:06 PDT
