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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Received on Thu Jun 30 2011 - 21:30:04 PDT
