A couple comments -- try turning MS off (set it to 0) and just let sander
calculate it via LCPO.
Also, SURFTEN and SURFOFF don't mean anything in PB. The PB variables are
CAVITY_SURFTEN and CAVITY_OFFSET.
Hope this helps,
Jason
On Sat, Apr 9, 2011 at 3:37 AM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> 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
> > > > >
> > > > > _______________________________________________
> > > > > 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
> > >
> >
> >
> >
> > --
> > 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
>
> _______________________________________________
> 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
Received on Sat Apr 09 2011 - 10:30:04 PDT
