Hi Sadaf,
I suppose there are a lot more than 502 residues; but a minimisation could well do nothing if you have inadvertently restrained the whole system.
Other than that I’d be thinking two atoms on top of each other or nearly so. Check your atomic coordinates.
Did you get an error message of any kind?
Best,
Ben
> On 10/10/2021, at 7:04 AM, 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 - 11:30:03 PDT
