Hi,
Have you tried using the modified pdb file as your topology file and then
reading in the trajectory (with trajin) in cpptraj?
That should probably work. If not, I refer back to Dan... ;)
--Marc
On 23 May 2012 09:06, colvin <colvin4367.gmail.com> wrote:
> Hi,
>
> I was thinking to generate the results that can be viewed using
> gnuplot and xmgrace for a trajectory, not only a pdb file. Since the
> HN need to replace by H, meaning that it's quite impossible to do it
> for a trajectory and i can only wait for the future release or bugfix
> right?
>
> Thanks and regards.
> Colvin
>
> On Wed, May 23, 2012 at 2:41 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > 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
> >>
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Received on Wed May 23 2012 - 01:30:04 PDT
