On Tue, 2014-06-17 at 19:16 -0400, Mahendra B Thapa wrote:
> Dear Amber Users
>
> Keeping in mind the previous post (
> http://archive.ambermd.org/201312/0094.html), my input file for the hbond
> analysis is like this:
>
> trajin sample.mdcrd
> # mdcrd is a NetCDF AMBER trajectory
> autoimage
> rms first mass .C,CA,N
> hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum
> run
> write solutehb.dat HB[solutehb]
>
> After running the cpptraj command (version V13.17), following warning
> message is seen:
> Warning: [hbond] Not all arguments handled: [ .N,C,H,O ]
> [run]
>
> Any suggestion in this issue might be a great help for me.
.N,C,H,O is not a valid mask. It doesn't contain any characters
required in every mask (it must have one of either :, ., or a single *
to select all atoms). As such, cpptraj does not recognize it as a mask
and doesn't know what to do with it.
See chapter 19 for details about the amber mask syntax.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 18 2014 - 08:30:02 PDT
