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???
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
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Received on Mon Apr 25 2011 - 11:00:02 PDT
