On Tue, Jan 05, 2021, Jatin Kashyap wrote:
>
>I am getting an error[1] upon performing minimization of drug-protein
>complex by using the AMBER tutorial[2].
You have two atoms on top of one another in your starting structure:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 9.2217E+09 O1 18
>
> BOND = 13750.1241 ANGLE = 10976.5308 DIHED = 2934.9414
> VDWAALS = NaN EEL = Infinity EGB = 60228.2741
> 1-4 VDW = 381037.7111 1-4 EEL = 14860.5376 RESTRAINT = 0.0000
Dave Cerutti pointed you to mdgx, but (for me) it's much simpler just
to use the cpptraj "check" command: it will print out short non-bonded
contacts and bad bonds (the two most common problems with initial
structures.)
cpptraj <prmtop file>
trajin <inpcrd file>
check
go
....dac
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Received on Tue Jan 05 2021 - 20:00:02 PST
