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.
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
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Received on Thu Mar 28 2013 - 02:30:02 PDT
