[gmx-users] how to select heavy atoms of Ligand

Giuseppina La Sala giuseppina.lasala2 at unibo.it
Tue May 20 14:26:18 CEST 2014

Dear Atsutoshi,

first you could make a new group by means of make_ndx:
make_ndx -f foo.gro (you complex) -o index_new.ndx
here when asked you should type:

group numer of your ligand & !a H*

For other analysis call the index already done with -n index_new.ndx

Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di atsutoshi.okabe at takeda.com [atsutoshi.okabe at takeda.com]
Inviato: martedì 20 maggio 2014 14.13
A: gmx-users at gromacs.org
Oggetto: [gmx-users] how to select heavy atoms of Ligand

Dear all,

I would like to make index file of heavy atoms of ligand by g_select command.
However, I don't know how to select heavy atoms of ligand.
I tried g_select -select "resname LIG and not name H" command, but it did not work.
Could you tell me any advice?

Atsutoshi Okabe

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