Thank you Jason,
The residue names for both ligands are same in solvated_complex.pdb ( I
thought I had changed them to BC1 and BC2 in complex.pdb before tleap but
looks like I didnt). I will change the residue names in complex.pdb and run
tleap again to create prmtop and inpcrd files to run MD.
Regards,
k
On Mon, Jul 2, 2012 at 10:43 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Jul 2, 2012 at 4:19 AM, kamlesh sahu <kamleshsemail.gmail.com
> >wrote:
>
> > Hello,
> >
> > I have simulated a complex containing chains and two lignads pdb ID
> > :4E1M.pdb . Topology files were created like this
> >
> > *tleap-1.in*
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > BC1 = loadmol2 BI-C-1-new.mol2
> > BC2 = loadmol2 BI-C-2-new.mol2
> > loadamberparams BI-C-1-new.frcmod
> > loadamberparams BI-C-2-new.frcmod
> > check BC1
> > check BC2
> > saveoff BC1 BI-C-1-new.lib
> > saveoff BC2 BI-C-2-new.lib
> > quit
> >
> > *tleap-2.in*
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > loadamberparams BI-C-1-new.frcmod
> > loadamberparams BI-C-2-new.frcmod
> > set default PBRadii mbondi2
> > loadoff BI-C-1-new.lib
> > loadoff BI-C-2-new.lib
> > complex=loadpdb indimer_complex.pdb
> > receptor=loadpdb indimer_receptor.pdb
> > BC1=loadmol2 BI-C-1-new.mol2
> > BC2=loadmol2 BI-C-2-new.mol2
> > saveamberparm complex complex.prmtop complex.inpcrd
> > saveamberparm receptor receptor.prmtop receptor.inpcrd
> > saveamberparm BC1 BC1.prmtop BC1.inpcrd
> > saveamberparm BC2 BC2.prmtop BC2.inpcrd
> > solvatebox complex TIP3PBOX 10.0
> > charge complex
> > addions complex Na+ 0
> > charge complex
> > addions complex Cl- 0
> > saveamberparm complex solvated_complex.prmtop solvated_complex.inpcrd
> > savepdb complex solvated_complex.pdb
> > quit
> >
> > After md simulations, I wish to calculate binding energies -
> > I used this command
> >
> > MMPBSA.py -O -i mmpbsa.in -o FINAL_MMPBSA_BI_C2.dat -sp
> > solvated_complex.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > BC2.prmtop -y prod*.mdcrd
> >
> > where mmpbsa.in is
> >
> >
> >
> -------------------------------------------------------------------------------------------------------------------------------------
> >
> > Input file for running PB and GB
> > &general
> > endframe=300, keep_files=2,
> > receptor_mask=:1-152-304, ligand_mask=:306
> >
>
> This mask is strange and most likely doesn't do what you think it does (in
> fact, there is no well-defined behavior for this). The double-range,
> :1-152-304 is not defined, and is rather arbitrarily parsed the same as
> :152-304 by both cpptraj and MMPBSA.py. If you want the receptor mask to
> be all residues between 1 and 304, the mask should be :1-304. If you want
> all residues between 1 and 304 except 152, you will need to break it into 2
> sections: :1-151,153-304.
>
> Keep in mind that the ligand and receptor masks are defined with respect to
> the complex topology file, NOT the solvated topology file. Therefore,
> every residue must be accounted for through the receptor and ligand masks.
> If your ligand is only a single residue and MMPBSA.py cannot figure out
> your masks automatically, that means your topology files are most likely
> incorrect. That is, your ligand and receptor topology files cannot be
> added together to get your complex topology file.
>
> You say you have 2 ligands, residues 305 and 306. If they are both the
> same residue name, then MMPBSA.py will automatically assign the ligand as
> residue 306 and assign residue 305 as part of the receptor. Note, that if
> you keep both ligands in the complex prmtop, you MUST assign one of them to
> the 'receptor' in MMPBSA.py if you wish to analyze them separately.
>
> If you want to strip out one ligand so it's not there while you're
> analyzing the other one, you'll need to modify your strip_mask to remove
> the desired ligand from solvated_prmtop (you'll need a corresponding
>
> You can use ante-MMPBSA.py in order to generate your complex, receptor, and
> ligand topology files from your solvated complex topology file, which will
> definitely be compatible with MMPBSA.py as long as you define your
> strip_mask and receptor_mask or ligand_mask correctly.
>
> I suggest analyzing your solvated topology file using xparmed.py with the
> "printDetails" button (or use the text version parmed.py) so that you can
> see exactly what atoms will be selected based on your input masks.
>
> HTH,
> Jason
>
> /
> > &gb
> > igb=5, saltcon=0.100,
> > gbsa=1,
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> >
> >
> --------------------------------------------------------------------------------------------------------------------------------------------
> >
> > one ligand is residue 305 in solvated_complex.pdb and other 306
> >
> > I am getting followeing error -
> >
> > Error: Sander output is missing values!
> > VDWAALS = ************* EEL = -10879.9496 EGB =
> > -7164.4331
> >
> >
> >
> > I had to specify the receptor and ligand mask because there was no best
> > guess for receptor and ligand mask.\
> >
> >
> > Could you please help me understand what is wrong.
> >
> > Thank you
> > k
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
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Received on Tue Jul 03 2012 - 01:00:03 PDT
