[From nobody Thu Nov 14 11:45:16 2013
Subject: make_ndx question
From: Senthil Kandasamy <senthilk@engin.umich.edu>
To: gmx_users@gromacs.org
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Date: 17 Dec 2002 16:32:31 -0500
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I have a question about make_ndx.

I  need to insert a large molecule into a system in a region with mostly
waters. I need to remove ALL the conflicting water molecules before
insertion.
 
Using a  simple atom based scan algorithm, I have an created an index
group named remove_clashes. This index file has indices of all the 
hydrogens and oxygens of water in the conflicting region. 

However, there are some waters with parts inside and parts outside the
conflicting region . My scan algorithm only catches the atoms inside the
conflicting region. This leaves some partial waters in the index file. I
need to remove the partial waters outside the conflicting region also.

so essentially i need to create a superset of remove_clashes which
basically includes the partial waters that are outside the conflicting
region. Then subtract this from the [system] using trjconv to create a
new system. 

How can make_index do this (or can it do this at all?)

It would essentially involve the following algorithm.

1. we know the atom numbers in remove_clashes.
2. get residue numbers for all these atoms.
3. get ALL the atoms from these residue numbers.
This should  create the necessary superset.

However, can make_ndx perform step 2 ? For some reason,I am not able to
come up with the right syntax to do it.

any help is really appreciated. Otherwise, I will have to do it
manually..sigh...


Senthil




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