I think that when ntr=1 you need to use restraintmask and restraint_wt
(section 2.6.4 amber manual). If you wanted to restrain a protein that
was 20 residues long, you could have something like:
ntr=1,
restraintmask=':1-20',
restraint_wt=5.0,
Maybe try something like that instead of having the RES...END section
at the end of your input file.
-Dan
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
>
> 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
> 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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Received on Thu Jul 22 2010 - 07:00:04 PDT
