AMBER Archive (2008)

Subject: SV: AMBER: ptraj, hbond and non-bonded contacts

From: Samuel Genheden (a03samge) (
Date: Mon Mar 17 2008 - 06:02:59 CDT

I have thought about it but I always postpone it since you have to fax the confidential agreement. I don't even know if we have a fax machine at work!
/ Samuel


Frċn: genom Jojart Balazs
Skickat: fr 2008-03-14 09:19
Ämne: Re: AMBER: ptraj, hbond and non-bonded contacts

Dear Sam,
did you try the ligplot program?
homepage -
SH2 domain complexed with a peptide containing phosphotyrosine (1sha) -
The program generates a text file, which includes the interaction, as well.
Hope this helps

Samuel Genheden (a03samge) wrote:
> Hello, Amber users
> I've have modelled a protein complex using a docking algorithm and now
> I'm performing an MD simulation of the docked complex. From the
> docking algorithm I have got a list of possible hydrogen bonds and a
> list of possible non-bonded contacts (carbon-carbon interactions). Now
> I want to track these contacts during the MD simulation...
> For the hydrogen contacts it is easy, I just use ptraj and the hbond
> facilities and it works fine.
> But how about the non-bonded contacts. Is it possible to use the hbond
> facility even for these contacts? As I see is the only problem how to
> define the acceptor atom. The acceptor command requires an hydrogen
> and the heavy atom which it is bonded to. Now I have carbons contacts
> that I want to keep track of, so which bonded atom should I use? My
> idea is just to take the heavy atom previous in the chain, e.g. a CB
> for a CG and CA for the CB. Is this a plausible solution?
> Best regards, Samuel
> _____________ NOD32 2946 (20080313) Információ _____________
> Az üzenetet a NOD32 antivirus system megvizsgálta.
> <>

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