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
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Received on Mon Jul 12 2010 - 07:30:04 PDT
