Start simple, and try to figure out the syntax for one command... Look at
all the warnings and messages.
A good step was also looking at the visualization with VMD, but what does
it mean that VMD "detected" hydrogen bondings? By eye?
I would also try calculation a simple distance and plotting that vs. time
(and also the distribution) to see if 3.5 angstroms is the appropriate
cutoff for these interactions.
distance d1 out d1.dat :1.N :6.OXT
> Actually when I visualize the system with VMD , I can visualize many
> hydrogen bondings
> but AMBER did not detected it
>
> > finally I ran this successfully, but I got all Zeros and that is strange!
> > I ran with NVT with Langevin thermostat and all interaction calculated
> >
> > hbond out N_H1_OXT.out donormask :1.N donorhmask :1.H1 acceptormask
> > :6.OXT dist 3.5 series h1
> > hbond out N_H2_OXT.out donormask :1.N donorhmask :1.H2 acceptormask
> > :6.OXT dist 3.5 series h2
> > hbond out N_H3_OXT.out donormask :1.N donorhmask :1.H3 acceptormask
> > :6.OXT dist 3.5 series h3
> >
> > what if I want to get the life time of the bond ?
> > should just write life time in the command ?!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 17 2015 - 10:00:04 PDT
