Hi,
The issue is with your topology file; specifically, all of the
backbone amide hydrogens in your system are named "HN" instead of "H"
(which AFAIK is the Amber standard and what cpptraj 'secstruct'
expects). There should probably be an option to set specific atom
names for each of the expected backbone atoms - this will be in a
future release and perhaps even a bugfix. For now, you can get around
this issue by renaming all of the "HN" atoms "H". I will send you a
PDB off-list where I have done this (based on the topology you
provided), and I successfully used it to calculate secondary structure
data.
Hope this helps,
-Dan
On Thu, May 17, 2012 at 4:06 AM, colvin <colvin4367.gmail.com> wrote:
> Dear all.
>
> I am having problem with secstruct in cpptraj, as the program couldn't
> read my mask for the residue (:1-460) and even if i didn't put the
> residue selection, the command still not working, with the output:
> Mask [:1-460] corresponds to 0 residues or Mask [*] corresponds to 0
> residues.
>
> i use radgyr and distance command in cpptraj for the same set of
> trajectories and prmtop file with the same mask, and they are working
> well. I have no idea what is wrong here. Pls advise.
>
> FYI, i already applied all the bugfix during compilation and the
> command used is exactly follow the one in manual (secstruct :1-460 out
> test and secstruct out test :1-460)
>
> Looking forward for your reply.
>
> Thanks and regards,
> Colvin
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 22 2012 - 12:00:03 PDT
