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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Received on Sun Aug 13 2006 - 06:07:02 PDT
