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

From: nicholus bhattacharjee <nicholusbhattacharjee.gmail.com>
Date: Mon, 12 Jul 2010 09:53:25 +0530

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)



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Received on Sun Jul 11 2010 - 21:30:03 PDT
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