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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>
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Received on Fri Jul 01 2011 - 07:30:04 PDT
