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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>
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Received on Fri Sep 24 2010 - 16:30:03 PDT
