It looks like it is an issue with ambpdb.
$ ambpdb -p VRQ6Imp.prmtop < VRQ6Imp.inpcrd > VRQ6Imp.stdin
| 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)
^
Aborted.
$
Any ideas on my next step, or is it the bug fix that needs to be installed?
Thanks!
> 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
>
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Received on Wed Mar 03 2010 - 12:00:04 PST
