Hi,
I've written a wrapper script which can be used to relax systems in
explicit solvent which you may find helpful:
https://github.com/drroe/AmberMdPrep
-Dan
On Sat, Oct 9, 2021 at 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 Thu Oct 14 2021 - 08:00:03 PDT
