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)
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Received on Wed Jul 21 2010 - 07:00:05 PDT
