Dear Amber users
I am trying to minimize a protein-ligand complex in which I kept a few of
crystal waters closer to the ligand in the starting structure.
I am using the following input for minimization:-
Min-01 minimize initial structure
&cntrl
imin=1, maxcyc=100000,
ntb = 1,
ntr = 1,
ntpr = 100,
ntwr = 100,
cut= 9.0,
restraint_wt=25.0,
restraintmask=':1-502',
/
But the minimization stops at the first step and I get the vdw energy
VDWAALS = ************* as mentioned below :-
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.4194E+11 2.4357E+10 6.9014E+12 O 8473
BOND = 372.9712 ANGLE = 1301.1419 DIHED =
6256.9248
VDWAALS = ************* EEL = -267129.8747 HBOND =
0.0000
1-4 VDW = 2633.8542 1-4 EEL = 17965.8509 RESTRAINT =
0.0000
Can you please suggest to me why it is happening and how should I fix it?
Thanks in advance.
Sadaf
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Received on Sat Oct 09 2021 - 11:30:02 PDT
