Hi,
You may have an easier time using the 'restraintmask' and 'restraint_wt'
namelist variables with ntr=1 (I almost always do), e.g.:
energy minimization
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 250,
cut = 10,
ntb = 1,
ntr = 1,
restraintmask = ':1-289',
restraint_wt = 5.0,
&end
Hope this helps,
-Dan
On Tue, Mar 25, 2014 at 8:16 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
>
> hi,
>
> I changed it to RES but still getting error:
>
> My input file is the following:
>
> energy minimization
> &cntrl
> imin = 1,
> maxcyc = 2000,
> ncyc = 250,
> cut = 10,
> ntb = 1,
> ntr = 1,
> /
> Hold the DNA-protein fixed
> RES 1 289
> END
> END
>
> in out I have:
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Hold the DNA-protein fixed
>
> rfree: Error decoding variable 1 3 from:
> RES
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
>
> I am using now AMBER11 and have no how to correct it.
>
> /Urszula
>
> > On Tue, Mar 25, 2014, Urszula Uciechowska wrote:
> >>
> >> My complex contains DNA and protein. I would like to use ibelly to keep
> >> frozen the complex and allowed water to move.
> >
> > I'd advise against that (but then I always do!) Consider using
> restraints
> > to
> > the initial position (ntr=1) rather than the belly.
> >
> >>
> >> energy minimization for DNA and protein
> >> &cntrl
> >> imin = 1,
> >> maxcyc = 2000,
> >> ncyc = 500,
> >> cut = 12,
> >> ntb = 1,
> >> ibelly = 1,
> >> /
> >> RES WAT
> >> END
> >> END
> >>
> >> LOADING THE BELLY ATOMS AS GROUPS
> >>
> >> ----- READING GROUP 1; TITLE:
> >> RES WAT
> >> Number of atoms in this group = 0
> >
> > Note that your group syntax is wrong, and is selecting zero atoms. See
> > the
> > chapter on group selections in the Manual.
> >
> >> NSTEP ENERGY RMS GMAX NAME
> >> NUMBER
> >> 1 -1.0972E+06 NaN 0.0000E+00 N 1
> >>
> >> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> >> 0.0000
> >> VDWAALS = -624.5497 EEL = -1096564.5563 HBOND =
> >> 0.0000
> >> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> >> 0.0000
> >
> > It's not clear what caused RMS to be NaN (not a number). You should
> > experiment with the input parameters (running short, say 10-step
> > simulations
> > with ntpr=1) until you can get something to work. The fact that you have
> > no
> > bond, angle, etc. energies is suspicious: I suspect that the code may
> well
> > have a bug if you set ibelly=1, but choose no atoms to be in the belly.
> >
> > Don't be afraid to experiment and try to see what will work.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 25 2014 - 10:00:03 PDT
