AMBER Archive (2006)

Subject: Re: AMBER: Format of mdcrd files

From: Mark Williamson (Mark.Williamson_at_imperial.ac.uk)
Date: Wed Aug 09 2006 - 09:32:06 CDT

Gobind Bisht wrote:
> Dear amber users,
> I want to analyse the mdcrd files of my
> simulation for distances between some specific grps vs time . What is
> the format in which this information is written into the mdcrd files and
> how do i extract it?
> Plz help
> thanx in advance
> Gobind Singh Bisht
> Department Of Biotechnology
> IIT Kharagpur, Kharagpur-721302
> West Bengal,

Have a look at the mdcrd format information;
http://amber.scripps.edu/formats.html#trajectory

but I suspect you are asking the wrong question and perhaps you should
be using the ptraj tool to extract this information. You need to read
around a bit. There is a useful summary of what ptraj can do at:

http://amber.scripps.edu/tutorial/ptraj/index.html

with specific attention to the distance command.

There is more than one way to do what you want to do; you could use the
VMD tool and set a distance measurement between two atoms; there was a
recent thread about it at:

http://amber.ch.ic.ac.uk/archive/200607/0038.html

regards,

Mark
http://dumb.ch.ic.ac.uk/~mjw99/
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