Yes I did that and it seems to run fine.
But problem is that if I run serially it put everything on head node and I have a time limit for 30 minutes for head node.
So I need to submit it to some queue
For that I am trying to make this script
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Monday, July 11, 2016 9:49:37 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA
how's about .out file?
Have you tried to run serially in your terminal (without submitting to
cluster)?
Hai
On Mon, Jul 11, 2016 at 4:46 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > 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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>
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Received on Mon Jul 11 2016 - 14:00:06 PDT
