Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md

From: nicholus bhattacharjee <nicholusbhattacharjee.gmail.com>
Date: Thu, 22 Jul 2010 05:37:35 -0400

Dear Jason,
                   Thank you for your help. Yes there are places in the
prod.rst file with values ********** (I have attached the prod.rst file). So
what should I do. I Should restart the simulation with ntxo=0 rather than
default value of 1 so that the results are written unformatted or you
suggest me do something else. I am eagerly waiting for your reply.

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


Received on Thu Jul 22 2010 - 03:00:03 PDT
Custom Search