Re: [AMBER] Error mmpbsa

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 1 Jul 2011 07:57:41 -0700

This is a limitation in the previous mmpbsa perl script. It removes
all output files by default ... do you know how to run sander or pbsa
by hand? They have the same syntax.

Ray

On Fri, Jul 1, 2011 at 7:21 AM, John S <s.john634.gmail.com> wrote:
>  This is my pbsa.in file , pbsa_com.1.out does not exist
>
> &cntrl
>  ntf    = 1,       ntb    = 0,
>  igb    = 10,      dielc  = 1.0,
>  cut    = 999.0,   nsnb   = 99999,
>  scnb   = 2.0,     scee   = 1.2,
>  imin   = 1,       maxcyc = 0,       ntmin  = 2,
>  &end
>  &pb
>  epsin  = 1.0,     epsout  = 80.0,
>  istrng = 0,       radiopt = 0,
>  sprob  = 1.4,     space   = 0.5,
>  maxitn = 1000,    npopt   = 1,
>  cavity_surften = 0.0072,    cavity_offset   = 0.00,
>  npbverb= 1
>  &end
>
>
> On Fri, Jul 1, 2011 at 2:00 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> File "rec.all.out" seems to be fine, but there are still no PB
>> energies in file "com.all.out" ... That's why you have the error
>> messages "Use of uninitialized value in multiplication value (*) at
>> ..."
>>
>> Can you show the new "pbsa_com.1.out" file? Make sure the file is
>> really new by removing the old ones if there is any.
>>
>> All the best,
>> Ray
>>
>> On Thu, Jun 30, 2011 at 9:17 PM, John S <s.john634.gmail.com> wrote:
>> > Now I placed the topology files of the receptor , ligand and complex in
>> the
>> > same directory.
>> >
>> > Use of uninitialized value in multiplication (*) at
>> > /usr/local/apps/amber9/src/m
>> > m_pbsa/mm_pbsa_statistics.pm line 1336.
>> > Use of uninitialized value in multiplication (*) at
>> > /usr/local/apps/amber9/src/m
>> > m_pbsa/mm_pbsa_statistics.pm line 1336.
>> > Use of uninitialized value in multiplication (*) at
>> > /usr/local/apps/amber9/src/m
>> > m_pbsa/mm_pbsa_statistics.pm line 1336.
>> > Use of uninitialized value in multiplication (*) at
>> > /usr/local/apps/amber9/src/m
>> > m_pbsa/mm_pbsa_statistics.pm line 1336.
>> >    No data for 0+0 PB PB 0
>> >
>> > rec.all.out file
>> >
>> > MM
>> > GB
>> > PB
>> > MS
>> > 1
>> >  BOND    =       21.4902  ANGLE   =      196.1867  DIHED      =
>> > 33.4947
>> >  VDWAALS =       26.0792  EEL     =       33.8852  EGB        =
>> > -16.2949
>> >  1-4 VDW =       62.7277  1-4 EEL =      -37.1338  RESTRAINT  =
>> > 0.0000
>> > surface area =     3992.1336
>> > corrected reaction field energy:      -57.625533
>> >  ECAVITY =       40.8084  EDISPER =        0.0000
>> > 2
>> >  BOND    =       19.5876  ANGLE   =      194.4075  DIHED      =
>> > 32.5736
>> >  VDWAALS =       27.9853  EEL     =       33.9554  EGB        =
>> > -16.2308
>> >  1-4 VDW =       64.1462  1-4 EEL =      -37.2666  RESTRAINT  =
>> > 0.0000
>> > surface area =     3986.0617
>> > corrected reaction field energy:      -57.698336
>> >  ECAVITY =       40.8005  EDISPER =        0.0000
>> >
>> >
>> > com.all.out
>> >
>> > MM
>> > GB
>> > PB
>> > MS
>> > 1
>> >  BOND    =       27.1075  ANGLE   =      525.9645  DIHED      =
>> > 565.9391
>> >  VDWAALS =      -25.4483  EEL     =        0.0000  EGB        =
>> > 0.0000
>> >  1-4 VDW =      137.9756  1-4 EEL =        0.0000  RESTRAINT  =
>> > 0.0000
>> > surface area =     4322.1199
>> >  ECAVITY =       45.0125  EDISPER =        0.0000
>> > 2
>> >  BOND    =       24.6461  ANGLE   =      524.6252  DIHED      =
>> > 564.9438
>> >  VDWAALS =      -24.3942  EEL     =        0.0000  EGB        =
>> > 0.0000
>> >  1-4 VDW =      139.8923  1-4 EEL =        0.0000  RESTRAINT  =
>> > 0.0000
>> > surface area =     4313.5184
>> >  ECAVITY =       44.9180  EDISPER =        0.0000
>> >
>> > MM
>> > GB
>> > PB
>> > MS
>> > 1
>> >  BOND    =        5.6172  ANGLE   =      329.7777  DIHED      =
>> > 532.4443
>> >  VDWAALS =      -41.6611  EEL     =        0.0000  EGB        =
>> > 0.0000
>> >  1-4 VDW =       75.2478  1-4 EEL =        0.0000  RESTRAINT  =
>> > 0.0000
>> > surface area =      407.1399
>> >  ECAVITY =        5.9205  EDISPER =        0.0000
>> > 2
>> >  BOND    =        5.0585  ANGLE   =      330.2177  DIHED      =
>> > 532.3702
>> >  VDWAALS =      -41.8098  EEL     =        0.0000  EGB        =
>> > 0.0000
>> >  1-4 VDW =       75.7461  1-4 EEL =        0.0000  RESTRAINT  =
>> > 0.0000
>> > surface area =      411.7751
>> >  ECAVITY =        5.8871  EDISPER =        0.0000
>> >
>> >
>> > On Mon, Jun 27, 2011 at 11:01 PM, Bill Miller III <brmilleriii.gmail.com
>> >wrote:
>> >
>> >> The Unit 8 Error message means that pbsa cannot find your prmtop file
>> that
>> >> you specified. Double check that you have properly defined the location
>> and
>> >> name of your complex prmtop file in the mm_pbsa.pl input file.
>> >>
>> >> -Bill
>> >>
>> >> On Mon, Jun 27, 2011 at 10:44 PM, John S <s.john634.gmail.com> wrote:
>> >>
>> >> > The following is my pbsa_com.1.out file.Is this related to  my input
>> >> file,
>> >> > why does MM=1 work with results on gas phase energies
>> >> >
>> >> >          -------------------------------------------------------
>> >> >          Amber 9  PBSA                   Scripps/UCSF 2006
>> >> >          -------------------------------------------------------
>> >> >
>> >> > | Run on 06/26/2011 at 23:17:31
>> >> >  [-O]verwriting output
>> >> >
>> >> > File Assignments:
>> >> > |  MDIN: pbsa.in
>> >> >
>> >> > | MDOUT:
>> >> > p4g_com.1.out
>> >> > |INPCRD: ./p4g_com.crd.1
>> >> > |  PARM: /p4
>> >> > |RESTRT:
>> >> > restrt
>> >> > |  REFC:
>> >> > refc
>> >> > | MDVEL:
>> >> > mdvel
>> >> > |  MDEN:
>> >> > mden
>> >> > | MDCRD:
>> >> > mdcrd
>> >> > |MDINFO:
>> >> > mdinfo
>> >> > |INPDIP:
>> >> > inpdip
>> >> > |RSTDIP:
>> >> > rstdip
>> >> >
>> >> >
>> >> >  Here is the input file:
>> >> >
>> >> > File generated by mm_pbsa.pl. Using
>> >> > PB
>> >> >  &cntrl
>> >> >
>> >> >  ntf    = 1,       ntb    =
>> >> > 0,
>> >> >  igb    = 10,      dielc  =
>> >> > 1.0,
>> >> >  cut    = 999.0,   nsnb   =
>> >> > 99999,
>> >> >  scnb   = 2.0,     scee   =
>> >> > 1.2,
>> >> >  imin   = 1,       maxcyc = 0,       ntmin  =
>> >> > 2,
>> >> >  &end
>> >> >
>> >> >  &pb
>> >> >
>> >> >  epsin  = 1.0,     epsout  =
>> >> > 80.0,
>> >> >  istrng = 0,       radiopt =
>> >> > 0,
>> >> >  sprob  = 1.4,     space   =
>> >> > 0.5,
>> >> >  maxitn = 1000,    npopt   =
>> >> > 1,
>> >> >  cavity_surften = 0.0072,    cavity_offset   =
>> >> > 0.00,
>> >> >  npbverb=
>> >> > 1
>> >> >  &end
>> >> >
>> >> >
>> >> >
>> >> >
>> >>
>> --------------------------------------------------------------------------------
>> >> >   1.  RESOURCE   USE:
>> >> >
>> >> >
>> >>
>> --------------------------------------------------------------------------------
>> >> >
>> >> > |
>> >> > Flags:
>> >> >
>> >> >
>> >> >  Unit    8 Error on OPEN: /p4g/
>> >> >
>> >> >
>> >> > On Mon, Jun 27, 2011 at 6:41 AM, Bill Miller III <
>> brmilleriii.gmail.com
>> >> > >wrote:
>> >> >
>> >> > > What error message is in the pbsa output files: pbsa_com.1.out ?
>> That
>> >> > > should
>> >> > > be where a more message is present.
>> >> > >
>> >> > > -Bill
>> >> > >
>> >> > > On Sun, Jun 26, 2011 at 11:29 PM, John S <s.john634.gmail.com>
>> wrote:
>> >> > >
>> >> > > > Dear Amber users,
>> >> > > > I am using Amber 9 for mmpbsa calculations (mm_pbsa.pl ), for MM
>> =1,
>> >> >  I
>> >> > > > get
>> >> > > > no errors whereas when I use PB=1 MM=1 , it gives the following
>> error
>> >> > .Is
>> >> > > > this related to my  input files or something to do with the
>> >> > installation
>> >> > > > .Please let me know
>> >> > > >
>> >> > > >  Unit    8 Error on OPEN: /p4g/
>> >> > > >        /usr/local/apps/amber9/exe/pbsa -O -i pbsa.in -o
>> >> pbsa_com.1.out
>> >> > > -c
>> >> > > > ./p4g_com.crd.1 -p /prep/p4g.prmtop not successful
>> >> > > >
>> >> > > >
>> >> > > > my pbsa.in file is as below
>> >> > > >
>> >> > > >  &cntrl
>> >> > > >  ntf    = 1,       ntb    = 0,
>> >> > > >  igb    = 10,      dielc  = 1.0,
>> >> > > >  cut    = 999.0,   nsnb   = 99999,
>> >> > > >  scnb   = 2.0,     scee   = 1.2,
>> >> > > >  imin   = 1,       maxcyc = 0,       ntmin  = 2,
>> >> > > >  &end
>> >> > > >  &pb
>> >> > > >  epsin  = 1.0,     epsout  = 80.0,
>> >> > > >  istrng = 0,       radiopt = 0,
>> >> > > >  sprob  = 1.4,     space   = 0.5,
>> >> > > >  maxitn = 1000,    npopt   = 1,
>> >> > > >  cavity_surften = 0.0072,    cavity_offset   = 0.00,
>> >> > > >  npbverb= 1
>> >> > > >  &end
>> >> > > >
>> >> > > > p4g_com.all.out
>> >> > > >
>> >> > > > MM
>> >> > > > GB
>> >> > > > PB
>> >> > > > MS
>> >> > > > 1
>> >> > > >  BOND    =       27.1075  ANGLE   =      525.9645  DIHED      =
>> >> > > >  565.9391
>> >> > > >  VDWAALS =      -25.4483  EEL     =        0.0000  EGB        =
>> >> > > >  0.0000
>> >> > > >  1-4 VDW =      137.9756  1-4 EEL =        0.0000  RESTRAINT  =
>> >> > > >  0.0000
>> >> > > > surface area =     4322.1199
>> >> > > >
>> >> > > > Thanks
>> >> > > > John
>> >> > > > _______________________________________________
>> >> > > > AMBER mailing list
>> >> > > > AMBER.ambermd.org
>> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> > > >
>> >> > >
>> >> > >
>> >> > >
>> >> > > --
>> >> > > Bill Miller III
>> >> > > Quantum Theory Project,
>> >> > > University of Florida
>> >> > > Ph.D. Graduate Student
>> >> > > 352-392-6715
>> >> > > _______________________________________________
>> >> > > AMBER mailing list
>> >> > > AMBER.ambermd.org
>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >> > >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Bill Miller III
>> >> Quantum Theory Project,
>> >> University of Florida
>> >> Ph.D. Graduate Student
>> >> 352-392-6715
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Fri Jul 01 2011 - 08:00:03 PDT
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