I believe that worked for the original incarnation of MMPBSA.py, but then
it was later modified to be more consistent with how masks were
traditionally selected elsewhere in Amber (cpptraj, mdin files, etc).
So we should update that in the manual. Thanks for letting us know!
-Bill
On Thu, Oct 20, 2022 at 10:42 AM Enrico Martinez <jmsstarlight.gmail.com>
wrote:
> Right, thank you!
> I will check it tomorrow with new decomposition analysis.
> BTW in amber manual I've found the following example
>
> print_res="20, 40-80, 200"
>
> Il giorno gio 20 ott 2022 alle ore 16:39 Bill Miller III
> <brmilleriii.gmail.com> ha scritto:
> >
> > There is no way to directly select all residues physically present
> around a ligand within the decomp script.
> >
> > For the print_res mask, you should be putting a colon between all
> residue numbers. So you should have something like this:
> >
> > print_res=":25:26:142:143:145:163:164:166:189"
> >
> > Honestly, my suggestion is just to write all residues to the output file
> and not worry about the print_res mask. Unless your system is incredibly
> large or you're very low on disk space, I'd just write them all to the file
> and then parse through the data afterward. The per-residue decomp results
> files are not particularly large or cumbersome to deal with, and you never
> know when you might want information about other residues' decomp results,
> also.
> >
> > -Bill
> >
> > On Thu, Oct 20, 2022 at 7:04 AM Enrico Martinez via AMBER <
> amber.ambermd.org> wrote:
> >>
> >> No actually it produces the same error, I've just tried like this:
> >> print_res=":166"
> >> I am quite sure that the residue 166 is present in the data.
> >> BTW could you suggest to me the atom mask selection (that would work
> >> with mmgbsa) to select all residues around the ligand (residue :lig in
> >> my case)?
> >>
> >> Il giorno gio 20 ott 2022 alle ore 12:27 Rafał Madaj
> >> <r.madaj.uw.edu.pl> ha scritto:
> >> >
> >> > Dear Enrico,
> >> >
> >> > You may be missing colon at print_res.
> >> >
> >> > Try adding it at the beginning of residue list like:
> >> >
> >> > print_res=":25,26,142,143,145,163,164,166,189"
> >> >
> >> > Best,
> >> >
> >> > Rafal
> >> >
> >> > On 20.10.2022 11:19, Enrico Martinez via AMBER wrote:
> >> >
> >> > Dear Amber users!
> >> > I am running mmgbsa with activated option for per-residue
> >> > decomposition expecting output for the selected residues:
> >> > &decomp
> >> > idecomp=1, dec_verbose=0,
> >> > csv_format=0,
> >> > print_res="25,26,142,143,145,163,164,166,189"
> >> > /
> >> > I've got the error:
> >> > raise DecompError('Mismatch in number of decomp terms!')
> >> > DecompError: Mismatch in number of decomp terms!
> >> > Error occurred on rank 0.
> >> >
> >> > I tried it then with just one residue
> >> > print_res="166"
> >> > but it produced the same error.
> >> > Finally without the print_res everything works OK.
> >> > What is the problem with the syntax assuming that all of the indicated
> >> > residues are well present in the output e.g. (the part of the log
> >> > obtained from ALL residues):
> >> > GLU 166 | R GLU 166 | 0.000 +/- 0.000 | -2.185 +/- 0.473 |
> >> > -4.331 +/- 1.396 | 4.152 +/- 1.347 | -0.325 +/- 0.032 |
> >> > -2.690 +/- 0.609
> >> > Many thanks in advance
> >> > Cheers
> >> > Enrico
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > --
> >> > dr inż. Rafał Madaj
> >> > Laboratorium Bioinformatyki Strukturalnej
> >> > Instytut Biologii Ewolucyjnej
> >> > Wydział Biologii UW
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > Bill Miller III
> > Assistant Professor of Chemistry
> > Truman State University
> > 417-549-0952
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Thu Oct 20 2022 - 09:00:03 PDT
