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
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Received on Thu Mar 28 2013 - 06:00:04 PDT
