AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA not successful

From: workalemahu berhanu (wgberhanu_at_gmail.com)
Date: Sun Aug 16 2009 - 12:22:01 CDT

Hi
yes I am using a cluser machine
 When I try to run /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in
-o pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop

I got

mikre_at_nid00092:~/PRION/MMPBSA> /u0/z/zz217/USG/amber/9.0/exe/pbsa -O
-i pbsa.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p
./GNNQQNYMYRSB.prmtop
Illegal instruction

When I checked the pbsa_com.1.out

there is no error message

the head and the tail of the pbsa_com.1.outfile is as follow

head

 -------------------------------------------------------
          Amber 9 PBSA Scripps/UCSF 2006
          -------------------------------------------------------

| Run on 08/16/2009 at 10:17:33
  [-O]verwriting output

File Assignments:
| MDIN: pbsa.in

-----

tail

mikre_at_nid00092:~/PRION/MMPBSA> tail pbsa_com.1.out
  SAS Surface: surface dots generated: 366

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0

thank you

On Sat, Aug 15, 2009 at 6:10 PM, <monnet.jordan_at_free.fr> wrote:
> Hi,
>
> Are you running the script using a cluster machine? If so, sometimes,
> the error message does not appear...
>
> When you try to run by hand:
>
> /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop
>
> What does it say? Is there any error message in pbsa_com.1.out?
>
> --jordan
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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