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)
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Received on Thu Mar 28 2013 - 07:30:02 PDT
