AMBER Archive (2008)

Subject: RE: AMBER: INPCRD error on open

From: Campbell, Patrick (pcampbell_at_msm.edu)
Date: Thu Mar 20 2008 - 12:02:12 CDT

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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