Thank you very much for your suggestion, it works!!
Thanks again! :)
On Wed, May 23, 2012 at 4:10 PM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> 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 - 02:30:02 PDT
