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 - 01:30:03 PDT
