Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond

From: qiao xue <xueqiaoup.gmail.com>
Date: Sat, 16 Jul 2011 11:21:04 +0800

Thanks very much, Roe.

I am using the Amber 10 and Ambertool1.2. The bugfix is 10.0 bugfixes.
And the compilers is Inter 11.1. The OS is linux.

My system is made up of 127 residues. I did 5ns. There are 2500 frames
in the md trajectory.

the input and out file are attached.

2011/7/14, Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Wed, Jul 13, 2011 at 7:54 PM, qiao xue <xueqiaoup.gmail.com> wrote:
>> When I am doing the Hbond analysis it often suffers the error
>> "segmentation fault".
>
> Can you please post more details about your system so we can try and
> reproduce the error?
> - What version of AmberTools are you using, what bugfixes have you
> applied, what compilers (and version) are you using and on what OS?
> - How large is your system (# atoms), how many frames is your
> trajectory, are box coords present? Ideally attach the topology file
> and 1 coordinate frame or restart file.
> - Post the exact ptraj input you are using, and optionally attach the
> output you are getting.
> Thanks!
>
> -Dan
>
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>


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Received on Fri Jul 15 2011 - 20:30:02 PDT
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