Hi,
We had noticed one behavior that if the ligand is not included in the
"print_residue" mask, the job for per-residue decomposition analysis never
seems to end. But with the ligand included it ends normally.
Is it a bug or we are expected to always include the ligand in the mask?
If the ligand is expected and not included then it should give some error.
Am I correct here?
Ligand not included and job never ends:
&decomp
idecomp=1, print_res="1-271"
dec_verbose=0,
/
Ligand included and job ends normally:
&decomp
idecomp=1, print_res="1-271; 272"
dec_verbose=0,
/
Here 272 is the ligand (small organic molecule).
On Sun, Feb 17, 2013 at 1:54 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Indeed, pairwise decomp should be idecomp=3 or 4. Thanks for the report,
> I'll fix it.
>
> --Jason
>
> On Sat, Feb 16, 2013 at 12:47 PM, George A. Khoury <gkhoury.princeton.edu
> >wrote:
>
> > Hi Everyone,
> > I noticed in this tutorial page:
> > http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
> >
> > the two portions describing per residue and pairwise energy
> decomposition.
> >
> > I think the input file for the pairwise decomposition has a very minor
> > mistake in it that could lead to unintentional confusion:
> >
> > mmpbsa_pairwise_decomp.in<
> >
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/mmpbsa_pairwise_decomp.in
> > >
> >
> > Pairwise GB and PB decomposition
> > &general
> > endframe=50, verbose=1,
> > /
> > &gb
> > igb=5, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100,
> > /
> > &decomp
> > idecomp=1, print_res="5; 30-40; 170-200"
> > dec_verbose=0,
> > /
> >
> > >From the AMBER manual for the pairwise demonstration the idecomp I
> > believe should be set to 3. If one ran the .in file here they would
> > get a per residue decomposition.
> >
> >
> > Thanks for your consideration and take care.
> > George Khoury
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 16 2013 - 21:30:02 PST
