That was very helpful
So, How can I detect the life time of these bonds ?!
On Sat, Oct 17, 2015 at 7:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Sat, Oct 17, 2015 at 10:56 AM, Hadeer ELHabashy
> <hadeer.elhabashi.gmail.com> wrote:
> > 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
>
> Have a look at the Amber mask syntax that cpptraj uses (Amber 15
> manual 29.1.6). The 'hbond' command actually does a reasonable job of
> detecting donors and acceptors on its own. For example, If you just
> wanted to look at hydrogen bonds between residues named GLU and
> residues named LYS you could do something like:
>
> hbond :GLU,LYS out nhb.dat avgout avghb.dat
>
> Hope this helps,
>
> -Dan
>
> >
> >
> >
> > 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 ?!
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Oct 17 2015 - 11:00:04 PDT
