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 .
Usually we first solvate the system and then replace water molecule
with counterion
to neutralize the system. Why did you do other way around?
On Tue, Jan 22, 2013 at 9:58 AM, Sun <sunbintyy.163.com> wrote:
> 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
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Received on Tue Jan 22 2013 - 01:30:04 PST
