Hi,
It still hangs. I brought it down to just GB, no PB or Decomp on 2 snapshots
and it still hangs.
Thanks,
Oliver
On 25 September 2010 00:16, Ray Luo <ray.luo.uci.edu> wrote:
> Does it hang if you turn off the PB for the decomposition?
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor in Computational
> Biochemistry and Molecular Biophysics
> Dept of Molecular Biology and Biochemistry
> Dept of Biomedical Engineering
> University of California, Irvine, CA 92697-3900
> Email: rluo.uci.edu Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/rayl/
> ==========================================
>
>
> On 9/23/2010 12:12 PM, Oliver Grant wrote:
> > Hi all,
> >
> > *Info:*
> > Amber 11
> > Ambertools 1.4
> > mm_pbsa.pl Last change: 16.01.2002
> > All tests past in mm_pbsa.pl and there were no errors during make
> install.
> >
> >
> > I have a mm_pbsa.pl calculation running on 1001 snapshots but it has
> frozen
> > right at the end. When I "top" mm_pbsa.pl is still running. Tailing the
> log
> > filegives this:
> >
> > Calc contrib for ./pl_com.crd.998
> > Calc MM/GB/SAS
> > Calc PBSA
> > Analyzing 998
> > Ana MM/GB/SAS
> > Ana PBSA
> > Calc contrib for ./pl_com.crd.999
> > Calc MM/GB/SAS
> > Calc PBSA
> > Analyzing 999
> > Ana MM/GB/SAS
> > Ana PBSA
> > Calc contrib for ./pl_com.crd.1000
> > Calc MM/GB/SAS
> > Calc PBSA
> > Analyzing 1000
> > Ana MM/GB/SAS
> > Ana PBSA
> >
> > ls -lart reveals:
> >
> > 635 Sep 22 19:03 pbsa_com.in
> > 81881 Sep 23 03:48 restrt
> > 55501716 Sep 23 03:48 pl_com.all.out
> > 434 Sep 23 03:48 mdinfo
> > 137561 Sep 23 03:48 LOG
> >
> > So nothing has happened since then (7 hours), can't find any errors in
> these
> > files. tailing pl_com.all.out gives:
> >
> > PB_BDC 109 8.859 -2.646 -5.006 -13.218 0.000
> > PB_BDC 110 8.082 -0.855 -7.877 -7.841 0.000
> > PB_BDC 111 6.441 -2.884 -11.269 -1.187 0.000
> > PB_BDC 112 9.865 -2.340 -13.257 -3.205 0.000
> > PB_BDC 113 6.269 -2.608 -8.184
> >
> > I've found this in the archive:
> >
> > "*Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > /amber/amber11/bin/sander -O -i pbsa_com.in -o pbsa_com.1.out
> -c
> > ./snapshot_com.crd.1 -p ./c_Q635A.prmtop not successful
> >
> > For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
> >
> >
> > If comment out the line:
> >
> > 596c596
> >
> > < print OUT " ipb = ${ipb}, inp = ${inp}, dielc =
> > ${dielc},\n";
> >
> > *
> >
> > *---
> >> #print OUT " ipb = ${ipb}, inp = ${inp}, dielc =
> > ${dielc},\n";
> >
> >
> > the program start but at the last step of the complex energy calculation
> >
> >
> > the output is freeze but the job still running. "*
> >
> > I had the same error about line 596 but fixed it (or so I thought) by
> > setting inp to 0 in my input file. Any other setting than 0 is
> incompatible
> > with PB decomp.
> > Any help/suggestions for things to try would be great.
> >
> > My mm_pbsa.in file:
> >
> > .GENERAL
> > PREFIX pl
> > PATH ./
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./pl_com.top.0
> > RECPT ./rec.top
> > LIGPT ./lig.top
> > GC 0
> > AS 0
> > DC 1
> > MM 1
> > GB 1
> > PB 1
> > MS 0
> > NM 0
> > ###############################
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1002
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 2
> > INP 0
> > NPOPT 1
> > CAVITY_SURFTEN 0.0072
> > CAVITY_OFFSET 0.00
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > SALTCON 0.005
> > ##################################
> > .DECOMP
> > DCTYPE 2
> > COMREC 1-144
> > COMLIG 145-148
> > COMPRI 1-148
> > RECRES 1-144
> > RECPRI 1-144
> > RECMAP 1-144
> > LIGRES 1-4
> > LIGPRI 1-4
> > LIGMAP 145-148
> > ##############################
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 1
> > GBSA 2
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > #################################
> > .MS
> > PROBE 0.0
> > #################################
> > .PROGRAMS
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Sat Sep 25 2010 - 05:30:03 PDT
