Hello Jason,
I used foloowing mmpbsa.in as input for binding energy calculation (one and
two are residue names in the pdb file for C and D respectively) -
Input file for running GB
&general
endframe=300, keep_files=2,
receptor_mask= ":1-152", ligand_mask= ":153-304"
strip_mask=":WAT:one:two:Cl-"
/
&gb
igb=5, saltcon=0.100,
gbsa=1,
/
The prmtop file was created like this
ource leaprc.ff99SB
source leaprc.gaff
loadamberparams leding-6-1-new.frcmod
loadamberparams leding-6-2-new.frcmod
set default PBRadii mbondi2
loadoff one.lib
loadoff two.lib
complex=loadpdb indimer_complex.pdb
receptor=loadpdb indimer_receptor.pdb
ligand=loadpdb indimer_ligand.pdb
one=loadmol2 leding-6-1-new.mol2
two=loadmol2 leding-6-2-new.mol2
saveamberparm complex complex.prmtop complex.inpcrd
saveamberparm receptor receptor.prmtop receptor.inpcrd
saveamberparm ligand ligand.prmtop ligand.inpcrd
saveamberparm one one.prmtop one.inpcrd
saveamberparm two two.prmtop two.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
Sorry I didnt mention these in my previous mails.
Regards,
kamlesh
---------- Forwarded message ----------
From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Tue, Jul 24, 2012 at 9:58 AM
Subject: Re: [AMBER] complex of protein dimer and two ligands simulated
MMPBSA.py error
To: AMBER Mailing List <amber.ambermd.org>
Hello,
The info about input files is given here
http://archive.ambermd.org/201207/0008.html
I striped C and D from the trajectories and used receptor prmtop (made of
residues A ) and ligand prmtop made from residues B only.... complex had
both. I get following message
ptraj found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/ptraj
sander found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/sander
Preparing trajectories with ptraj...
Error! Ptraj failed. Check coordinate and topology files for the complex.
If I dont strip ligands C and D (both small molecules present in 4E1M.pdb),
then I get following message
ptraj found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/ptraj
sander found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/sander
Preparing trajectories with ptraj...
50 frames were read in and processed by ptraj for use in calculation.
Starting calculations...
Starting gb calculation...
calculating ligand contribution...
calculating receptor contribution...
calculating complex contribution...
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -23008.7269 EGB = -3393.3682
binding energy calculation is successful when I use residues A, C and D to
make receptor.prmtop and residue B to make ligand.prmtop (complex
containing all ABCD). What I want MMPBSA.py to calculate is binding
energies between A and B ignoring C and D ( trajectories have C and D also
.... I already have the binding energies of A and B from trajectories where
C and D small molecules were absent ... I am using amber 10)
Thank you for your support
Regards,
kamlesh
On Mon, Jul 23, 2012 at 8:51 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Jul 23, 2012 at 3:51 AM, kamlesh sahu <kamleshsemail.gmail.com
> >wrote:
>
> > Hello,
> >
> > I have simulated a a dimer (protein A and B) in complex with two ligands
> C
> > and D. While making prmtop and inpcrd files, protein A and B together was
> > treated as receptor and C abd D were treated as ligands (see below for
> the
> > input file plz). Now I wish to calculate the binding energy of A and B.
> >
>
> I don't see an input file.
>
>
> > 1- Can I use the same trajectories where I provide protein A as receptor
> in
> > receptor_mask and protein B as ligand ? Will this require creation of new
> > prmtop files where I feed A as receptor and B as ligand to tleap ?
> >
>
> Yes you can use the same trajectories (so long as you understand the
> approximation that you're making -- namely that the conformational states
> sampled by a subset of your system is the same as in both the bound and
> free states). Yes, you will need a complex prmtop that has the residues of
> both A and B, a receptor prmtop that is just residues A, and a ligand
> prmtop that is just residues B.
>
> 2- Do I need to strip C and D from the trajectories by adding residue names
> > in strip_mask list ?
> >
>
> If they are not in either the receptor or ligand, yes you do.
>
>
> >
> > Thank you
> > Regards,
> > kamlesh
> >
>
> I'm confused. Do you still have an error? Just horribly wrong binding
> free energies? Is everything working, just the C/D, or is nothing working?
>
> 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
>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Mon Jul 23 2012 - 19:00:02 PDT
