On Mon, Oct 15, 2012 at 12:55 AM, Chris Chris <alpharecept.yahoo.com> wrote:
> I am trying to minimize a strecture that contains an anzyme and it's
> substrate. The complex was created by using Vina to dock the substrate to
> the enzyme. I followed the steps in the antechamber tutorial to make the
> inpcrd and prmtop files.
>
> I tried the same exact protein without the docked ligand and it ran
> without error. The message below says I should try turning off SHAKE, but
> will that affact my results down the road here?
>
It will probably not affect your results. The minimization should keep
hydrogen-heavy atom bonds at their equilibrium distance (since they are
typically very stiff).
my min.in file:
>
> min 1st time for ctz 2ps
> &cntrl
> imin=1,maxcyc=5000,ncyc=500,
cut=8.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=100,
> ntr=1,
> /
> Putting restraints on residues 1-305
> 500.0
> RES 1 306
> END
> END
>
Just bringing your attention to the fact that your comment (residues 1-305)
does not match your residue selection (1-306).
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 2.6120E+05 4.0553E+03 5.6572E+05 HD21 1590
>
> BOND = 31311.4597 ANGLE = 30018.2823 DIHED =
> 2992.1159
> VDWAALS = 98941.5229 EEL = -109489.5411 HBOND =
> 0.0000
> 1-4 VDW = 181774.5442 1-4 EEL = 13899.4160 RESTRAINT =
> 11752.4888
> EAMBER = 249447.8000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 5 780 1589 1590
> *** Especially for minimization, try ntc=1 (no shake)
>
Your gradient here is HUGE (on the order of 10^5). And your restraint
energy is also way too large for 500 steps of minimization. Double-check
your -ref file (is it the same as your inpcrd file? most of the time it
should be) and double-check your starting coordinates to make sure they
make sense (visualize them to see if you can find any obvious steric
clashes). This looks as though your reference coordinates are too far away
from your initial coordinates, which is introducing huge forces and
destroying your system.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 15 2012 - 05:30:03 PDT
