There is nothing in it.
It is just empty.
In my script I generate two files .err and .out
#BSUB -n 16
#BSUB -q parallel
#BSUB -W 168:00
#BSUB -J mmpbsa_WT_NH2
#BSUB -P prmt
#BSUB -o %J.out
#BSUB -e %J.err
So while running it stops after 2 minutes and i get blank .err file
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Monday, July 11, 2016 9:41:40 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA
it seems that you got lots of trouble with MMPBSA.
I suggest you to
- read AMBER tutorial, follow it and reproduce it.
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial3_py-5Fscript_&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=RyzYf2t1iheX3X5v5cYjh5hSoIL2cIiT6gWkJCDIAjA&s=KYP0sLhFNqZRrs4jdRz1IYFH4tNw4ApHBoIOJUNiz_k&e=
- Did your amber version pass the tests?
- Per your previous emails about MMPBSA: were you issue solved? If not,
have you tried to follow corresponding instruction?
- more specific: what does 'crash' mean? What is exact error message?
Hai
On Mon, Jul 11, 2016 at 4:31 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> I am trying to do mmpbsa calculation using following script
>
>
> set amber = $AMBERHOME/bin/MMPBSA.py.MPI
>
> #Write input below
> cat > mmpbsa.in << EOF
> Input file for running PB
> &general
> startframe=1, endframe=58750, interval=2,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
>
> #Execute MMPBSA job serial version
>
> mpirun -np 16 $amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp
> PRMT7_WT_NH2.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> peptide.prmtop -y *.crd
>
> so the script crashes and there seems to be no error in the output file.
> I don't know where I am committing mistake.
> kindly help me out
>
> _______________________________________________
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> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=RyzYf2t1iheX3X5v5cYjh5hSoIL2cIiT6gWkJCDIAjA&s=CESrs1nJpQJE5Wue8X3UxoFLJZFq6ze-iVgOP9KKE_8&e=
>
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Received on Mon Jul 11 2016 - 14:00:04 PDT
