when you re-run it I suggest you use ioutfm=1 to use the NetCDF format.
On Mon, Apr 25, 2011 at 11:04 AM, Vaibhav Jain <xtreme.vaibhav.gmail.com>wrote:
> ya nw I got it...
>
> my 707 frame of mdcrd file is corrupted. :(
>
> Actually the size of file is in GB, so was trying to split into small
> chunks.
> Nw when I upload that chunk.mdcrd in vmd it stops at 706 frame.
>
> I think again I have to run simulation.
>
> Thanks alot for ur valuable suggestions.
>
> On Mon, Apr 25, 2011 at 11:23 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > 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
> > _______________________________________________
> > 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 - 12:00:05 PDT
