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
> >
> > _______________________________________________
> > 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
>
--
**************************************************************************************************************************
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
Received on Thu Apr 07 2011 - 05:00:03 PDT
