Hi,
I have a receptor with a proline at N-terminal. Before running
secstruct in cpptraj, i rename HN to H in my pdb file and used it as a
topology file. But i'm having problem with this particular receptor
that start with proline, it comes with 2 HN. I tried to rename HN1 to
H1 and HN2 to H2 but the program stop with segmentation fault and
without any error message. I also tried to rename it to H2 and H3, but
it is still stop with segmentation fault and without any error
message. What is the Amber standard for backbone amide hydrogens for
N-terminal proline?
Pls advise.
Thanks and regards,
colvin
On 5/23/12, 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 Tue Jul 10 2012 - 01:30:04 PDT
