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
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Received on Thu Apr 07 2011 - 04:30:03 PDT
