AMBER Archive (2006)

Subject: Re: AMBER: helix content during my simulation

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Mon Feb 06 2006 - 09:39:59 CST

The code is written in a very rough way, coz it's just for personal use.
Anyway, hope it can help.
To use it, you need to
1. have a dssp binary under your "~/bin/" directory, or you may modify
the third argument of DSSP class in tom.py to suit your case.
2. place the two attached python script files under the same directory.
3. assign values to the variables in the dssp.py file, before the
"import sys" line.

If you know a little about python, it should be easy to do all this.
Good luck!

Mingfeng

julien wrote:
> Thanks,
>
> can send me yours python script? please
>
> thanks for advance
>
>
>> Usually, I convert snapshots to PDB files from the produced trajectory,
>> and then perform dssp analysis on each PDB file.
>> This procedure can be automated by a simple python script.
>>
>> Best,
>> Mingfeng
>>
>> julien wrote:
>>
>>> Dear all,
>>>
>>> I want to "observe" the alpha helix content in my peptide during the
>>> simulation.
>>> Differents persons use the dssp program. How using the dssp program with
>>>
>> amber ?
>>
>>> is-it with MMTSB or with ptraj or carnal?
>>>
>>> Sincerely yours
>>>
>>> best regards
>>> julien
>>>
>>>
>>>
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>
>
>


  • text/x-python attachment: tom.py

  • text/x-python attachment: dssp.py
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