Hello,
On Wed, Mar 3, 2010 at 2:11 PM, Jamie Romnes
<jromnes.student.physics.ucdavis.edu> wrote:
> Hello,
>
> In attempting my first constant ph AMBER9 experiment, I've hit a snag in
> generating the necessary cpin file. It appears there may be an issue with
> cpnutil.pl?
> Here's my output:
>
> $ ambpdb -p Model.prmtop < Model.inpcrd | cpinutil.pl > cpin
> | New format PARM file being parsed.
> | Version = 1.000 Date = 02/18/10 Time = 14:50:45
>
> lib-4001 : UNRECOVERABLE library error
> A READ operation tried to read past the end-of-file.
>
> Encountered during a sequential formatted READ from unit 5
> Fortran unit 5 is connected to a sequential formatted text file
> (standard input).
> Current format: 30 FORMAT(20A4)
> ^
> Use of uninitialized value in ord at
> /share/apps/amber-9/pathscale/exe/cpinutil.pl line 29.
> Use of uninitialized value in pattern match (m//) at
> /share/apps/amber-9/pathscale/exe/cpinutil.pl line 31.
> Use of uninitialized value in string eq at
> /share/apps/amber-9/pathscale/exe/cpinutil.pl line 31.
> Use of uninitialized value in string eq at
> /share/apps/amber-9/pathscale/exe/cpinutil.pl line 31.
> Use of uninitialized value in array dereference at
> /share/apps/amber-9/pathscale/exe/CPin.pm line 131, <GEN0> line 1.
> Use of uninitialized value in numeric lt (<) at
> /share/apps/amber-9/pathscale/exe/cpinutil.pl line 68, <GEN0> line 1.
> Use of uninitialized value in array dereference at
> /share/apps/amber-9/pathscale/exe/CPin.pm line 131, <GEN0> line 1.
> Use of uninitialized value in numeric lt (<) at
> /share/apps/amber-9/pathscale/exe/CPin.pm line 57, <GEN0> line 1.
> Use of uninitialized value in length at
> /share/apps/amber-9/pathscale/exe/CPin.pm line 512, <GEN0> line 1.
> Use of uninitialized value in concatenation (.) or string at
> /share/apps/amber-9/pathscale/exe/CPin.pm line 518, <GEN0> line 1.
It's hard to be certain about what is breaking here, since this
command calls two amber programs (ambpdb and cpinutil.pl). The stdout
of ambpdb is piped to cpinutil as stdin. Try running the ambpdb
command by itself. Does this fail? Do you get a PDB out of it? I
don't think cpinutil.pl is broken, as it's a simple perl script that
should run the same anywhere perl is correctly installed.
The end-of-file fortran error makes me think there was a problem in
ambpdb first that then translated into cpinutil.pl not knowing what to
do with a blank stdin.
As a side note, if you plan on doing constant pH MD, I would direct
you to make sure that bugfix.47 (for amber9) is applied. This is
especially true if your system has multiple titrating residues that
may interact with one another.
Good luck!
Jason
--
---------------------------------------
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
Received on Wed Mar 03 2010 - 12:00:02 PST
