Hi,
On Tue, Jul 10, 2012 at 2:06 AM, colvin <colvin4367.gmail.com> wrote:
> 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
Can you send me the modified files (off-list) so that I can try to
reproduce the error?
> 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?
The standard names for the N-terminal PRO amine (this is not really an
amide since the N is not bonded to a carbonyl) hydrogens are H2 and
H3, neither of which would be recognized by 'secstruct' since it
expects backbone amide hydrogen atoms named 'H'. You could perhaps try
renaming one or the other to 'H', but I wouldn't recommend this.
In my opinion with larger proteins it's not so crucial to get the
secondary structure content of the terminii since they tend to be
somewhat disordered anyway; whenever I use secstruct I usually leave
off the first and last 5 or so residues. However, you shouldn't be
seeing that segfault so send me the files off-list and I'll take a
look at them. Thanks!
-Dan
>
> 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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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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http://home.chpc.utah.edu/~cheatham/
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Received on Tue Jul 10 2012 - 07:30:02 PDT
