Dear Jason,
I do have mobile ions Na+ in my system. But looking at the
trajectory file in vmd I dont think it is the Na+ ions. You asked me to use
nscm. But it has the default value of 1000 and I have not changed. Then also
looking at the trajectory in vmd shows that some residues are drifting..I
dont know the reason.
On Thu, Jul 22, 2010 at 5:36 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> 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
Received on Thu Jul 22 2010 - 07:00:05 PDT
