Dear David and AMBER
At first stage I did minimization with restraints on heavy atoms except
water and hydrogen which was resulting in LINMIN failure. As per previous
suggestion on same it has been suggested that minimizer could not search
any more conformation lower than the present ones but one can go for MD
further. In next step I did complete minimization of the same system which
stops at 30 steps. I have attached output file for review please. How to
run cpptraj for structure check and how to analyse?
thank you
Sadaf
On Wed, Jul 3, 2019 at 12:49 PM David A Case <david.case.rutgers.edu> wrote:
> 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 Thu Jul 04 2019 - 12:00:02 PDT
