On Tue, Jan 22, 2013, Sun wrote:
>
> I have a ligand which comprises of 36 atoms and its net charge is -1. I
> have generated the force field parameter files ,i.e., prepin and frcmod
> files, for the ligand with antechamber correctly. One Na+ as counterion
> was added to the ligand for neutralizing the nagetive charge , then the
> systen was solvated in TIP3P water model with the water buffer being 8
> angstroms . The system was then subjected to a minimization with the
> input file reads as following :
> &cntrl
> imin=1,maxcyc=2000,ncyc=1500,
> cut=8.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=50,
> drms=0.05
> ntr=1,
> restraint_wt=2.0,
> restraintmask=":1"
> /
> There were two points seemed weird in the output file of the
> minimizaton : First , the minimization finished without achieving
> the criteria " drms < 0.05" nor the maxcyc was reached ( it stopped
> at step 1600 with the message "RESTARTED DUE TO LINMIN FAILURE" ) .
> Second, the energy information about the previous 1550 steps which
> were accomplished were exactly the same, i.e., from NSTEP1 to NSTEP2,
> nothing changed. it seems that the minimization does not do any effect
> at all .
The default Amber minimizer, does not work correctly with SHAKE, and so can
easily get stuck in a system that is mostly water. We generally only use
solvated minimization to eliminate bad contacts in preparation for MD
equilibration. So you can probably go ahead with such MD studies (although
using only a 8 Ang. buffer is probably too small, and you are likely to
encounter problems...consider using a larger buffer.
...dac
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Received on Tue Jan 22 2013 - 05:30:03 PST
