Hi Daniel
Thanks for your response.
I have issues the command as:
hbond all_frames out nhb.dat avgout series uuseries avghb_frame.dat
Using, this I am getting data for each frame in form of o (no H-bond) and 1
(H-bond)..
But I want interactions as well for 1 (H-bond present) like
#Acceptor DonorH Donor Frames
Frac AvgDist AvgAng
ILE_5.O LEU_9.H LEU_9.N 652
0.6520 2.8749 159.9352
LYS_8.O SER_11.HG SER_11.OG 589 0.5890
2.7123 162.9552
and that too I want interaction between ligand and protein and not among
protein -protein residues.
Kindly suggest.
On Thu, Oct 10, 2019 at 8:30 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If you want data on each individual hydrogen bond detected you need to
> use the 'series' keyword (optionally with the 'uuseries' and/or
> 'uvseries' keywords) to tell cpptraj to generate a data set for each
> detected hydrogen bond; these sets will have a 1 every time the
> associated hydrogen bond is present and 0 when not. See the manual for
> full details.
>
> -Dan
>
> On Tue, Oct 8, 2019 at 2:40 AM shivangi agarwal
> <shiviagarwalpharma.gmail.com> wrote:
> >
> > Thanks
> > But there is no such command to write H bond interactions
> >
> > On Tue, Oct 8, 2019 at 11:53 AM Elvis Martis <elvis_bcp.elvismartis.in>
> > wrote:
> >
> > > Hello
> > > You may want to look at this tutorial
> > > http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
> > > Best Regards
> > >
> > >
> > >
> > > On Tue, 8 Oct 2019 at 11:51, shivangi agarwal <
> > > shiviagarwalpharma.gmail.com>
> > > wrote:
> > >
> > > > Hello all
> > > >
> > > > Is there any tool available which can write H-bond interactions of
> each
> > > of
> > > > the frame generated from MD trajectory?
> > > > Like we have H-bond analysis function in VMD but it write no of
> hydrogen
> > > > bonds for each frame.
> > > > I want name of residues which are showing H-bond interactions for
> each
> > > > frame.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > With regards
> > > > Shivangi Agarwal
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Received on Sat Oct 12 2019 - 22:30:01 PDT
