On Tue, Jul 02, 2019, Sadaf Rani wrote:
>
>I have used the same minimisation file output file to look for the energy
>it seems that energy is stable now as in dat file attached. I did complete
>minimization from this system as following command
>sander -O -i min_all.in -p complex.prmtop -c complex.inpcrd -r
>complex_min_all.rst -o complex_min_all.out
>
>*However it stops at 30 steps:*
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 30 1.7222E+07 5.7664E+05 2.5970E+08 CG2 4394
>
> BOND = 138230.7732 ANGLE = 10176.6357 DIHED =
>7716.9429
> VDWAALS = 17385498.1326 EEL = -614341.8893 HBOND =
> 0.0000
> 1-4 VDW = 277507.6838 1-4 EEL = 17256.8798 RESTRAINT =
> 0.0000
First, is there any indication in the output file of a LINMIN failure?
(You mentioned that in the subject of the email, but above you just say
that the program stops after 30 steps--is there something in the output
file you are not showing us?)
Second, You still have very bad van der Waals terms, suggestive of a bad
initial conformation, so bad that minimization is not able to fix it.
Have you run "checkstructure" in cpptraj on the initial coordinates?
That is likely to point to problems with your starting structure.
...dac
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Received on Wed Jul 03 2019 - 05:00:03 PDT
