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
>> >
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Jul 01 2011 - 08:00:03 PDT
