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
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Received on Thu Apr 07 2011 - 12:30:03 PDT
