AMBER Archive (2008)

Subject: RE: AMBER: INPCRD error on open

From: Campbell, Patrick (pcampbell_at_msm.edu)
Date: Thu Mar 20 2008 - 13:35:37 CDT

Hello Dr. Simmerling,

Thanks for your insight into my error - I have made the changes (the flags were not all on the same line), resubmitted the job, and will appraise you of the results as they present themselves.

Thanks again and do have a great day!
Patrick

________________________________________
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling
Sent: Thursday, March 20, 2008 11:10 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: INPCRD error on open

it's hard to tell from this version, but are all of your flags on the same line as the mpirun?
if not, then you need a continuation slash (\) at the end of the partial commands.
my guess is that sander isn't getting the stuff after the first line and that's why it's
looking for the default name of "inpcrd".

On Thu, Mar 20, 2008 at 1:02 PM, Campbell, Patrick <pcampbell_at_msm.edu> wrote:
Hello Dr. Simmerling,

Here are the scripts for sander and the called minimization.

SANDER SCRIPT

mpirun -np 2 $AMBERHOME/exe/sander -O -i Zeta_ntrl_wat_min1.in
-o Zeta_ntrl_wat_min1.out -c Zeta_ntrl_wat.inpcrd -p Zeta_ntrl_wat.prmtop -r Zeta_ntrl_wat_min1.rst
-ref Zeta_ntrl_wat.rst

Zeta_ntrl_wat_min1.in Script

cat Zeta_ntrl_wat_min1.in
204aa: initial minimization Protein + solvent + ions
 &cntrl
imin  =1,
maxcyc=1000,
ntpr=5,
ntr   = 1,
&end
Group input for restrained atoms
100.0
RES 1 204
END
END

I did check the folder and there is a file called Zeta_ntrl_wat.inpcrd in the directory. Do let me know if to send it as an attachment in a follow up email to you.

Thanks again for all your assistance and do have a great day!

Patrick

________________________________________
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling
Sent: Thursday, March 20, 2008 9:23 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: INPCRD error on open

it might help if you send your sander script so we can see
what you specified. without that we can only guess.
do you actually have a file called "inpcrd" in that directory?
On Thu, Mar 20, 2008 at 11:17 AM, Campbell, Patrick <pcampbell_at_msm.edu> wrote:
A pleasant good morning to all,

I am getting the following error from the mdout file after a failed
minimization run on a neutralized hydrated protein.

 1.  RESOURCE   USE:
------------------------------------------------------------------------
--------
| Flags: MPI
 getting new box info from bottom of inpcrd
 Unit    9 Error on OPEN: inpcrd

Can anyone suggest a possible strategy towards the correction of this
problem?

Thanks much.
Patrick
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