AMBER Archive (2007)

Subject: Re: AMBER: intra-molecular h-bonds in ptraj

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Thu Jan 04 2007 - 14:11:36 CST

There might be something wrong with the ptraj's interpretation of the
selection command.

Please use
donor mask :MTS_at_O1
acceptor mask :MTS_at_N1 :MTS_at_H7

instead of
donor MTS O1
acceptor MTS N1 H7

If you cannot fix the problem by doing so, please let me know.

Jianyin

On 1/4/07, lily ferreira <lily_1_mart_at_yahoo.fr> wrote:
>
>
>
> Dear members,
> I am triying to mesure intra-molecular bonds using
> ptraj. My input file is:
>
> trajin file1.mdcrd
> rms first out file1.rms :GSU_at_C1,C2,C3,C4,C5
> donor MTS O1
> acceptor MTS N1 H7
> hbond distance 4.0 donor acceptor series hbond
>
> but I obtain the following message
>
> "data was sorted, intra-residue interactions are NOT included"
>
> How can I list intra-molecular h-bonds?
>
>
> Thanking
> you in advance
>
>
>
>
>
>
>
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>
>
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