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
That's not the set cmd to use.
Bill
> 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.
>
> Thanks and regards,
> Aneesh
>
>
>
>
> On Thu, Mar 28, 2013 at 11:02 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > On 3/27/2013 10:01 PM, aneesh cna wrote:
> > > Dear Amber users,
> > >
> > > I would like to generate a PDB file with atom radii in the B-factor
> > field.
> > > Is there a way to do this in Amber?
> > If your residues match the standard templates, you can use leap's
> > loadPdb and savePdb, plus I believe there is a 'set' cmd, try 'help
> > set', maybe there is an argument like pdbradii.
> >
> > Bill
> > >
> > > Thanks in advance
> > >
> > > Regards
> > > Aneesh
> > > _______________________________________________
> > > 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
> >
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Received on Fri Mar 29 2013 - 16:30:02 PDT
