That was great, I figured out a problem was the atoms numbering
what if I want to use residue names instead of numbers
is this correct ?!
Acceptor MET O Donorh ALA H donor ALA N is this equilvelant to this
On Sat, Oct 17, 2015 at 6:41 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> 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 ?!
>
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Received on Sat Oct 17 2015 - 10:00:06 PDT
