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
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Received on Tue Mar 25 2014 - 07:00:02 PDT
