Thanks for the reply. For now, I have done it with PDB2PQR server. I will
definitely try what Daniel has suggested.
Thanks once again to all
regards
Aneesh
On Thu, Mar 28, 2013 at 7:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> FYI If you are starting with an Amber topology file you can get the GB
> radii (and charges) printed to a PDB in the B-factor and occupancy
> columns respectively with cpptraj/ptraj using 'trajout <filename> pdb
> dumpq'.
>
> -Dan
>
> On Thu, Mar 28, 2013 at 6:46 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Thu, Mar 28, 2013 at 5:25 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> >
> >> Dear Bill,
> >>
> >> Thanks for the immediate reply.
> >>
> >> As you suggested, I have tried running leap with the following
> commands..
> >>
> >> **************************************
> >> source leaprc.ff99SB
> >> source leaprc.gaff
> >> native = loadpdb Model.pdb
> >> set native PBradii bondi
> >> savepdb native Radii.pdb
> >> quit
> >> **************************************
> >>
> >>
> >> But, unfortunately leap didn’t add atom radii to the saved PDB file.
> The
> >> log file shows the following messages.
> >>
> >>
> >>
> >>
> **************************************************************************************
> >> -I: Adding /usr/local/amber12//dat/leap/prep to search path.
> >> -I: Adding /usr/local/amber12//dat/leap/lib to search path.
> >> -I: Adding /usr/local/amber12//dat/leap/parm to search path.
> >> -I: Adding /usr/local/amber12//dat/leap/cmd to search path.
> >> -s: Ignoring startup file: leaprc
> >> -f: Source leap_2.in.
> >>
> >> Welcome to LEaP!
> >> Sourcing: ./leap.in
> >> ----- Source: /usr/local/amber12//dat/leap/cmd/leaprc.ff99SB
> >> ----- Source of /usr/local/amber12//dat/leap/cmd/leaprc.ff99SB done
> >> Log file: ./leap.log
> >> Loading parameters: /usr/local/amber12//dat/leap/parm/parm99.dat
> >> Reading title:
> >> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> >> incl.02/04/99
> >> Loading parameters: /usr/local/amber12//dat/leap/parm/frcmod.ff99SB
> >> Reading force field modification type file (frcmod)
> >> Reading title:
> >> Modification/update of parm99.dat (Hornak & Simmerling)
> >> Loading library: /usr/local/amber12//dat/leap/lib/all_nucleic94.lib
> >> Loading library: /usr/local/amber12//dat/leap/lib/all_amino94.lib
> >> Loading library: /usr/local/amber12//dat/leap/lib/all_aminoct94.lib
> >> Loading library: /usr/local/amber12//dat/leap/lib/all_aminont94.lib
> >> Loading library: /usr/local/amber12//dat/leap/lib/ions94.lib
> >> Loading library: /usr/local/amber12//dat/leap/lib/solvents.lib
> >> ----- Source: /usr/local/amber12//dat/leap/cmd/leaprc.gaff
> >> ----- Source of /usr/local/amber12//dat/leap/cmd/leaprc.gaff done
> >> Log file: ./leap.log
> >> Loading parameters: /usr/local/amber12//dat/leap/parm/gaff.dat
> >> Reading title:
> >> AMBER General Force Field for organic molecules (Version 1.4, March
> 2010)
> >> add. info. at the end
> >> Loading PDB file: ./Model.pdb
> >> total atoms in file: 2612
> >> Leap added 2866 missing atoms according to residue templates:
> >> 2866 H / lone pairs
> >> *default_name: PBradii is a non-existent attribute for a unit.
> >> Unit attributes: head, tail, restype, box, cap, name*
> >> Writing pdb file: Radii.pdb
> >> Converting N-terminal residue name to PDB format: NGLY -> GLY
> >> Converting C-terminal residue name to PDB format: CSER -> SER
> >> Quit
> >>
> >>
> ************************************************************************************************
> >>
> >>
> >> Can you help to figure out what went wrong with the leap commands.
> >>
> >
> > I don't think leap can do what you want it to do (at least not easily).
> The
> > PBRadii are actually never stored but actually determined when the
> topology
> > file is written.
> >
> > VMD might be able to do this more easily.
> >
> > HTH,
> > Jason
> >
> > --
> > 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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 28 2013 - 22:30:04 PDT
