Dear Jason,
Sorry for late response. I have attached the input. I have recompiled
two/three times after modification but every time i am unable to run job
properly.
On Fri, Apr 8, 2011 at 12:34 AM, Jason Swails <jason.swails.gmail.com>wrote:
> What does your input file look like?
>
> On Thu, Apr 7, 2011 at 4:53 AM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com>wrote:
>
> > Dear Sir,
> >
> > I did the same and it runs properly for com and rec but for ligand it is
> > again showing error as follows-
> >
> > Calc contrib for ./ok8_R4_rec.crd.6
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > Calc MS
> > Died at /usr/local/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 662,
> > <PDB>
> > line 36.
> > Calc contrib for ./ok8_R4_lig.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > No radius found for Br8 35 in residue R4 1
> >
> > Regards
> >
> > On Thu, Apr 7, 2011 at 4:33 PM, Bill Miller III <brmilleriii.gmail.com
> > >wrote:
> >
> > > You will need to add the radius of bromine to the
> $AMBERHOME/src/mm_pbsa/
> > > mm_pbsa_calceneent.pm file. Also, do not forget to re-compile
> > > mm_pbsa.plafterward or else you will not see any changes when running
> > > the program.
> > >
> > > Good luck!
> > >
> > > -Bill
> > >
> > > On Thu, Apr 7, 2011 at 3:52 AM, Kshatresh Dutta Dubey
> > > <kshatresh.gmail.com>wrote:
> > >
> > > > Dear all,
> > > >
> > > > I am using amber10 on SUSE 11.3 operating system. When i am
> calculating
> > > > mm_pbsa using mm_pbsa.pl, it is showing error like " *No radius
> found
> > > for
> > > > Br8 6180 in residue*" . Here, Br8 is bromine atom whose atom no is
> > 6180
> > > > in
> > > > pdb. However, i can successfully calculate mm_pbsa for other ligands
> > > > without
> > > > Bromine.
> > > > Can anyone suggest me to get rid of this issue? I will be grateful
> for
> > > > every
> > > > help. I am attaching my log file.
> > > >
> > > > Thanks in advance
> > > >
> > > > --
> > > >
> > > >
> > >
> >
> **************************************************************************************************************************
> > > > Kshatresh Dutta Dubey
> > > > Senior Research Fellow (SRF)
> > > > Biophysics Unit,
> > > > Department of Physics
> > > > DDU Gorakhpur University
> > > >
> > > > _______________________________________________
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> > > > 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
> > >
> >
> >
> >
> > --
> >
> >
> **************************************************************************************************************************
> > Kshatresh Dutta Dubey
> > Senior Research Fellow (SRF)
> > Biophysics Unit,
> > Department of Physics
> > DDU Gorakhpur University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
**************************************************************************************************************************
Kshatresh Dutta Dubey
Senior Research Fellow (SRF)
Biophysics Unit,
Department of Physics
DDU Gorakhpur University
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Received on Sat Apr 09 2011 - 04:00:02 PDT
