Re: [AMBER] How to get the information of hydrophobic contact?

From: g t <>
Date: Tue, 13 Mar 2012 17:39:44 +0000


in order to get detailed info from amber contacts might the following
command work for you?
contacts first out Contacts_proteinALL.out distance 5.0 ":ALA, :CYS,:PHE,

This should give you contacts inbetween all the hydrophobic residues
listed. the number includes intra & intermolecular contacts. if you wish to
subtract intra molecular contacts, you will have to run the command again
with every individual residue from the above mask and subtract from total
given in the example above.

contacts first out Contacts_proteinALL.out distance 5.0 ":94"

hope this makes sense.

best regards,

On 8 March 2012 03:03, qiao xue <> wrote:

> Hello all,
> I read a paper which use AMBER MD simulations. Their analysis contain
> the hydrophobic contacts. They define the hydrophobic contact for a
> pair of the hydrophobic side chains of residues(Ala, Cys, Phe, Leu,
> Met, Ile, Val) was considered to be formed when a minimal distance
> between the center of mass of any pair of residues is less than 5.4A.
> I read the Ambertools help and find a command "contacts". But it seems
> that it could not do the analysis above. So would I ask a question
> that how to do this analysis?
> The other question is that if I want to constrain the residues with
> mask. e.g. I just want to know the interaction among Ala, Cys, Phe.
> Can I write like this: :Ala, Cys, Phe.CA?
> Thanks!
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Received on Tue Mar 13 2012 - 11:00:03 PDT
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