AMBER Archive (2006)

Subject: Re: AMBER: Interbox interactions

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Tue Oct 17 2006 - 11:03:18 CDT

Thanks. Will try these.
austin-

>
>> Does anyone know of a script/programme that can be used to perform
>> interbox contact analyses from an MD trajectory? I would like to find
>> out
>> whether my solute (dodecasaccharide) is making contacts with its images.
>
> There are a couple of ways to do this.
>
> (1) Use the "distance" command in ptraj(); this implicitly images (unless
> disabled) and will give insight into the shortest distance measured. So,
> if you look at the end-to-end distance of your sugar, assuming it is not
> folded, you could see short distances to the periodic images.
>
> distance e1 :1 :10 out end-to-end.dat
>
> (2) Build a series of PDB files with shifted images... [See the archives
> for a script to do this, but basically...]
>
> ptraj prmtop << EOF
> trajin restrt.1
> trajout restrt_111.pdb pdb
> image origin xoffset 1 yoffset 1 zoffset 1
> EOF
>
> ...will build a PDB file imaged and shifted by one unit cell in each
> direction... Then you can manually look at the interactions.
>
> --tom
>
>
>
>
>
>
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Austin B. Yongye
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263

"...then, we learn better in a free spirit of curiosity, than under fear
and compulsion..." -St. Augustine of Hippo
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