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
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Received on Mon Apr 25 2011 - 09:00:04 PDT
