I suggest you to use this tleap in further cases where u can write a
com_solvated.pdb while generating topology. Dont worry about tutorial it is
upto you either you can use cpptraj to generate a corresponding
com_solvated.pdb or use tleap at the beginning. The best way to identify
the residues is to change the Full_mini.rst to Full_Mini.pdb using ambpdb
by something like ~/amber12/bin -p com_solvated.top <Full_Mini.rst>
Full_Mini.pdb
Download this Full_Mini.pdb delete water and ions in Chimera or PyMol. Open
it in Maestro or LigPlot or PoseView. Note down the residues which are in
active site. Identify your ligand in com_solvated.pdb and then put the mask
of all as suggested by me earlier.
Use the below tleap to generate corresponding com_solvated.pdb during
running tleap
source leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
receptor = loadPDB rec.pdb
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Cl- 0
solvateBox complex TIP3PBOX 8.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit
On Wed, May 28, 2014 at 2:03 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, May 28, 2014 at 1:07 AM, Arunima Shilpi <writetoash28.gmail.com
> >wrote:
>
> > Dear Sir
> >
> > "Open your com_solvated.pdb file. Identify the mask which denote the
> > ligand.
> > Suppose residue mask is 556 and if you open the minimized pdb you can
> > identify some crucial residues such as X1, X2 take out their atom mask.
> >
> > In the print residue put like this "556,X1,X2"
> >
> >
> > Say for example you ligand mask is 905 and your crucial amino acid
> residues
> > are 902 and 903. Then in print residue put like this "905,902,903"
> > Thats it."
> >
> >
> > As per your suggestion to go through com_solvated.pdb file , I have not
> > generated com_solvted.pdb file. Moreover in the totutorial its saying to
> > select residue from comlex.prmtop file.
> >
> > I did go through the complex.pdb file but I am not getting which residue
> to
> > slect.
> >
> >
> > Kindly guide me as to how to go ahead with residue selection.
> >
>
> Write PDB file from your complex prmtop and an inpcrd or a restart file
> (either ambpdb or cpptraj will do this for you). Go through that PDB and
> look at the residues you want to obtain pairwise energies for. Add those
> residues to print_res.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researche
> r
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed May 28 2014 - 05:30:03 PDT
