GROUP input always needs a start and an end. If you only want residue 94,
then your GROUP input should be changed as indicated below:
On Sat, Jun 25, 2011 at 4:22 AM, "André C. Stiel" <
andre.stiel.tuebingen.mpg.de> wrote:
> Hey Bill,
>
> Thanx for your answer,
> i tried a test with idecomp = 1:
> """"""""""""""""""""
> gfp:
> &cntrl
> imin = 1,
> maxcyc = 25,
> ncyc = 10,
> ntb = 1,
> ntr = 0,
> cut = 10.0,
> idecomp=1,
> /
> &end
> Group 1
> RES 94
> END
>
Group 1
RES 94 94
END
END
Note the second 94 is always looked for, so if it's not present then it
won't be read. Also note the second END, which tells Amber to stop reading
group inputs.
HTH,
Jason
""""""""""""""""""""""
>
> But what I get out is:
> """"""""""""""""""""""""""""
> LOADING THE DECOMP ATOMS AS GROUPS
>
> ----- READING GROUP 1; TITLE:
> &end
> ***PROBLEMS WITH GROUPGrou 1 0 0 0 0 0 0 0
> 0 0 0 0 0 0*******
>
> GRP 1 RES 94 TO 94
> Number of atoms in this group = 24
> ----- READING GROUP 2; TITLE:
>
>
> rfree: End of file on unit 5
> """""""""""""""""""""""""""""""
> Is it possible idecomp does not work with minimization (imin=1)?
> Im a absolute newbie, so i´m rather lost here....
>
> cheers
> andré
>
>
>
> Am 24.06.2011 um 14:24 schrieb Bill Miller III:
>
> > Using "idecomp" sounds like a way to get the answer/energy you want, and
> > that is probably the way I would go about it, also.
> >
> > -Bill
> >
> > On Fri, Jun 24, 2011 at 3:14 AM, "André C. Stiel" <
> > andre.stiel.tuebingen.mpg.de> wrote:
> >
> >> hi,
> >>
> >> kind of a simple problem (i hope): i did a minimization using AMBER 11:
> >>
> >> &cntrl
> >> imin = 1,
> >> maxcyc = 2500,
> >> ncyc = 1000,
> >> ntb = 1,
> >> ntr = 0,
> >> cut = 10.0
> >> /
> >>
> >> In the .out file I get the energy information over the whole protein.
> What
> >> should I do to just get the energies of a single amino acid?
> >> Is "idecomp" the way? Mind, I don´t want any fancy stuff, I just want to
> >> know how "happy" this particular amino acid is energy wise.
> >>
> >> Thanx a lot!
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> 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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Received on Sat Jun 25 2011 - 13:30:03 PDT
