This is a sign of a bad initial structure. The output tells you the atom
with highest forces (the gmax line). You should load the structure into a
program like Vmd and check that region. You can also use checkstructure in
cpptraj (see the manual).
If the structure is very bad it can be hard to minimize. Your restraints
may also keep it from moving.
On Sat, Oct 9, 2021, 2:00 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
> 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 - 15:30:02 PDT
