Dear all:
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 .
So, could anyone give me some help or advice ? I am very appreciated for your help.
-Sun
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 22 2013 - 01:30:03 PST
