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
>>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 30 2011 - 23:30:03 PDT
