Constant pressure doesn't apply to minimization, i.e. box
won't change. I believe that with min ntb is effectively
auto-set to 1 if a box is present in the prmtop; in any
case ntp has no effect.
I note that you call your 2nd min.in 'simulated annealing',
but it is the same as the 1st file, so it is not clear if
the problem arises during min or dynamics.
Is the molecule ok after min? If not, try min w/out belly
to see what happens.
Also when starting dynamics, be sure to equilibrate carefully
per the varied advice in the equilibration FAQ on the amber web.
Bill Ross
I am having a very difficult time with PBC conditions for a protein
complex. I am attempting to take some minimized coordinates from the
protein + box and do simmulated annealing. I know that the box
coordinates can change (in constant P situations) and I think this is
the case. As soon as I start the simmulated annealing, my protein is
distorted, and I'm guessing it has to do with the transfer of box
coordinates. The box coordinates from the topology file and the
minimization output are the same. Here's my input, let me know if you
can help.
minimization:
Complete optimization solute and solvent
&cntrl
imin=1, maxcyc=15000, ibelly=1,
scee=1.2, idiel=1, cut=8.0,
nsnb=20, ntpr=50, ntp=2, ntb=2,
&end
Belly definition
RES 27 32
RES 40
RES 43 47
RES 49 54
RES 56 62
RES 64 72
RES 107
RES 110
RES 134 4798
END change (in constant P situations) and I think this is
the case. As soon as I start the simmulated annealing, my protein is
distorted, and I'm guessing it has to do with the transfer of box
coordinates. The box coordinates from the topology file and the
minimization output are the same. Here's my input, let me know if you
can help.
minimization:
Complete optimization solute and solvent
&cntrl
imin=1, maxcyc=15000, ibelly=1,
scee=1.2, idiel=1, cut=8.0,
nsnb=20, ntpr=50, ntp=2, ntb=2,
&end
Belly definition
RES 27 32
RES 40
RES 43 47
RES 49 54
RES 56 62
RES 64 72
RES 107
RES 110
RES 134 4798
END S 107
RES 110
RES 134 4798
END
END
Received on Wed Feb 28 2001 - 15:50:16 PST
