Re: [AMBER] error in hydrogen bond

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 7 Jun 2014 07:24:26 -0400

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
Received on Sat Jun 07 2014 - 04:30:02 PDT
Custom Search