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
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AMBER mailing list
AMBER.ambermd.org
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Received on Mon Jun 27 2011 - 20:30:03 PDT
