AMBER Archive (2008)

Subject: RE: AMBER: stripping water from a restart file

From: CHAMI F. (fatima.chami_at_durham.ac.uk)
Date: Thu Oct 23 2008 - 16:59:03 CDT

 

________________________________

From: owner-amber_at_scripps.edu on behalf of Bill Ross
Sent: Thu 23/10/2008 19:13
To: amber_at_scripps.edu
Subject: RE: AMBER: stripping water from a restart file

> > What error msg was given?
> >
> > Unit 30 Error on OPEN: dimer-vac_md.rst_1000000=3D20
>
> That unit number looks fishy. What args did you run sander with?
>
> $AMBERHOME/exe/sander.MPI -O -i mdin -p dimer.prmtop -c =
> dimer-vac_md.rst_1000000 -r jar_1.rst -o jar_1.out -x jar_1.mdcrd=20
>
> I suspect that the topology file generated after stripping water using =
> rdparm is different form the topology file generated by Leap

I guess the unit number is ok.. the problem isn't the format of the
file, it's that it can't be opened. Try

% ls -l dimer-vac_md.rst_1000000

-rw------- 1 dch1fc dch 2956 2008-10-22 21:54 dimer-vac_md.rst_1000000

it has a readable permission

I found a bug in my script 'cd' command ...so sander tried to open a file in a diffrent path...its solved now thanks

I am trying to run an SMD simulation with 4 residues in vacuum and i got the following message :
 Must have more residues than processors!

and job stopped ...does it mean I cant run this simulation on this system

best wishes

Fatima

in the directory you're running in to see if it is really there and
has readable permission.

Bill
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