Hello,
My comments are below:
On Thu, Jul 22, 2010 at 9:16 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi,
>
> I am minimization a protein complex where I have decided to keep all the
> crystal waters - this might be one of my problems though. I want to start a
> minimization of the crystal water
>
Did you visualize the system to see if there are any obvious conflicts?
>
> Minimization of water molecules rest is fixed
> &cntrl
> imin = 1,
> maxcyc = 50000,
> ncyc = 25000,
> ntb = 0,
> ntr = 1,
> igb = 0,
> cut = 12
> /
> Hold protein fixed
> 500.0
> RES 1 802
> END
> END
>
> The first of the minimization the energies explode which I presume are due
> to bad vdw interaction -clashing I have tried to change the dt=0.00001 but
>
dt is meaningless in a minimization. This is the correct approach only for
molecular dynamics. It would help to see the results from the mdout file so
we can see any error message (if any) that you received trying to run the
simulation.
Good luck!
Jason
> that did not solve the problem. I would prefer not to remove too many of
> the
> crystal waters but could I try just to minimize the hydrogens in the
> system?
> I have tried selection like
>
> ATOM '!.H'
>
> instead of RES but this is a wrong syntax how to fix this?
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jul 22 2010 - 08:00:03 PDT
