[gmx-users] make_ndx question

David spoel at xray.bmc.uu.se
Tue Dec 17 21:49:52 CET 2002

On Tue, 2002-12-17 at 22:36, Senthil Kandasamy wrote:
> From: Senthil Kandasamy <senthilk at engin.umich.edu>
> To: gmx_users at gromacs.org
> Subject: make_ndx question
> Date: 17 Dec 2002 16:32:31 -0500
> 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.
Why don't you use genbox?

> 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.
No, either your program should do it, or genbox can do it.

> any help is really appreciated. Otherwise, I will have to do it
> manually..sigh...
> Senthil
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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