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.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Carlos Simmerling
> Sent: Thursday, March 20, 2008 9:23 AM
> To: amber.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.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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Received on Fri Apr 18 2008 - 21:12:37 PDT
