On Sat, Oct 17, 2015 at 11:57 AM, Hadeer ELHabashy
<hadeer.elhabashi.gmail.com> wrote:
> That was very helpful
> So, How can I detect the life time of these bonds ?!
As indicated in the manual entry for the hbond command, use the
lifetime analysis command (page 600). An example specific to hbond
analysis is given.
Hope this helps,
-Dan
>
>
> 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 ?!
>> >>
>> >> _______________________________________________
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>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
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>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
-------------------------
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)
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Received on Sat Oct 17 2015 - 12:00:02 PDT
