Why do you have coordinates that are becoming too large for the fixed format
restart file? Do you have mobile ions included? The COM translations
should be removed every nscm steps, so a small species not bonded to
anything must be drifting too far away, in which case I don't think it
should be part of your system at all. You can check your mdcrd file to see
which part is drifting too far away.
Good luck!
Jason
On Thu, Jul 22, 2010 at 7:41 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear Jason,
> I have just checked AMBER 10 manual. nxto=0 is no loger
> supported with that. so what should I do.
>
> On Wed, Jul 21, 2010 at 12:33 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > You do not need to create a cpin file from a cprestrt, the cprestrt will
> > work just as well. As for the ambpdb error, does your restart file have
> any
> > ********* entries from something migrating too far? How does the restart
> > file look when you visualize it? ambpdb is failing on a floating point
> read,
> > so i'm guessing it's a problem with a coordinate.
> >
> > Visualizing will probably help you diagnose the problem.
> >
> > Good luck!
> > Jason
> >
> > --
> > Jason Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> >
> > On Jul 21, 2010, at 9:37 AM, nicholus bhattacharjee <
> > nicholusbhattacharjee.gmail.com> wrote:
> >
> > > Dear Jason,
> > > Thank you for your kind help. I have some other
> > problems
> > > also. As you can see from my earlier I am running 10 nano seconds
> > constant
> > > pH simulation in two batches of 5 nano seconds each. Now when the 5
> nano
> > > second run is over I am able to generate the properties (like rmsd,
> > trajout)
> > > from the trajectory file. But both my output files csprestrt and
> prod.rts
> > > files are corrupted for example
> > >
> > > if I do
> > >
> > > $ ambpdb -p prmtop <prod.rst> x.pdb
> > >
> > > its giving error msg
> > >
> > > | New format PARM file being parsed.
> > > | Version = 1.000 Date = 07/06/10 Time = 17:54:02
> > > At line 624 of file _ambpdb.f (unit = 5, file = 'stdin')
> > > Fortran runtime error: Bad value during floating point read
> > >
> > > I am unable to understand what is the problem. My prod.out file is
> giving
> > > the analysis of the whole trajectory. Please help...
> > >
> > > On Mon, Jul 12, 2010 at 10:04 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> > >
> > >> Hello,
> > >>
> > >> The cprestrt looks quite strange... However, this step described in
> the
> > >> manual is only necessary if you feel the need to get rid of all the
> > >> extraneous zeroes that crop up because you're not titrating the
> maximum
> > >> number of residues (50). sander simply dumps the contents of the
> whole
> > >> &cnstph namelist to the cprestrt file, then reads the contents of the
> > >> &cnstph namelist when it reads the cpin file. Therefore, you can just
> > use
> > >> the cprestrt as the cpin file directly without any modification.
> > >>
> > >> Good luck!
> > >> Jason
> > >>
> > >> On Mon, Jul 12, 2010 at 12:23 AM, nicholus bhattacharjee <
> > >> nicholusbhattacharjee.gmail.com> wrote:
> > >>
> > >>> Dear community,
> > >>> I am running a constant pH MD of 10 nano
> seconds
> > >> in
> > >>> a remote cluster. Since there is a cut of time of 72 hrs for user I
> > have
> > >> to
> > >>> break the simulation into two parts of 5 ns each. Now after the first
> 5
> > >> ns
> > >>> simulation is over I have go cprestrt file from the simulation.
> > According
> > >>> to
> > >>> the manual I have to conver this cprestrt file to cpin2 file with the
> > >>> following command
> > >>>
> > >>> $ cpintil.pl cprestrt > cpin2
> > >>>
> > >>>
> > >>> But it is showing the following errors
> > >>>
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in numeric lt (<) at
> > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > >>> Use of uninitialized value in array dereference at
> > >>> /usr/local/amber9/exe/CPin.pm line 186.
> > >>> Can't call method "AtomCount" on an undefined value at
> > >>> /usr/local/amber9/exe/CPin.pm line 61.
> > >>>
> > >>>
> > >>> I am unable to understand what to do. Please help. I am attaching the
> > >>> cprestrt file.
> > >>>
> > >>> --
> > >>> Nicholus Bhattacharjee
> > >>> PhD Scholar
> > >>> Department of Chemistry
> > >>> University of Delhi
> > >>> Delhi-110007 (INDIA)
> > >>> Phone: 9873098743(M)
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>>
> > >>
> > >>
> > >> --
> > >> Jason M. Swails
> > >> Quantum Theory Project,
> > >> University of Florida
> > >> Ph.D. Graduate Student
> > >> 352-392-4032
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Nicholus Bhattacharjee
> > > PhD Scholar
> > > Department of Chemistry
> > > University of Delhi
> > > Delhi-110007 (INDIA)
> > > Phone: 9873098743(M)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
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Received on Thu Jul 22 2010 - 05:30:04 PDT
