Re: [AMBER] error in hydrogen bond

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Sat, 7 Jun 2014 19:13:18 +0530

Use CPPTRAJ as suggested by Jason put something like
trajin md50.mdcrd
hbond :1-198 out hbond.dat (I am not sure)

Otherwise convert your trajectory to NetCDf. Upload corresponding topology
or pdb in VMD with the coordinate. Go to Analysis plugin there you will
found H-Bond analysis plugin where u can see H bond occupancy over
simulation period.

Either way choice is urs. But try both.




On Sat, Jun 7, 2014 at 4:54 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Sat, Jun 7, 2014 at 12:48 AM, Arunima Shilpi <writetoash28.gmail.com>
> wrote:
>
> > Dear Sir
> >
> > I executed ptraj command for hbond analysis as follow
> >
> > ptraj 3pta_DRG_solvated.top <ptraj_hbond.in >analyse_hbond.out
> >
> > The ptraj_hbond.in file is as follow
> >
> > trajin md2.mdcrd
> >
> > donor mask :905.O5
> > donor mask :905.OD1
> > donor mask :905.O7
> > donor mask :905.O
> >
> > acceptor mask :454.O :454.H
> > acceptor mask :475.O :475.H
> > acceptor mask :905.O :905.H
> > acceptor mask :882.OD1 :882.H
> >
> >
> > hbond distance 3.5 angle 120.0 includeself donor mask acceptor mask
> > neighbor 2 series \ hbond
> >
> >
> > While running the command i got the following error
> >
> > PTRAJ: Processing input from "STDIN" ...
> >
> > PTRAJ: trajin md2.mdcrd
> > Checking coordinates: md2.mdcrd
> > Rank: 0 Atoms: 187380 FrameSize: 4553359 TitleSize: 81 NumBox: 3
> Seekable 1
> >
> >
> > PTRAJ: donor mask :905.O5
> > Mask [:905.O5] represents 1 atoms
> >
> > PTRAJ: donor mask :905.OD1
> > Mask [:905.OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!
> > WARNING in ptraj, donor: No atoms selected (:905.OD1), ignoring...
> >
>
> ‚ÄčThis is about as clear of an error message as Amber prints. There is no
> atom named OD1 in residue 905. You need to play around with your masks
> until you get them right (the ambmask program can help with this).
>
> Given the problems that you are having with ptraj's hbond command, I highly
> recommend you use cpptraj from AmberTools 14 and look into the hbond
> command there. It does a good job of predicting what the hydrogen bond
> donors and acceptors are so all of the donor and acceptor commands are
> unnecessary.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Thanks & Regards;
Soumendranath Bhakat
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Received on Sat Jun 07 2014 - 07:00:02 PDT
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