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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 02 2012 - 07:00:03 PDT
