[gmx-users] genion to not continuous solvent

Diego Enry diego.enry at gmail.com
Wed Nov 2 02:33:16 CET 2005

Dear list,
I am having an issue with genion and hope you guys could help me.

   Genion is working great , but one of the water molecules it
replaces was supposed to be a part of a water-mediated H-bond like the
one we see at HIV protease, so I really want that molecule to remain
over there.

   The problem is that genion does not allow me to simply hide this
water molecule by creating a new .ndx entry (14 SOL_but_not_my_water) 
without having to reorder and renumber the SOL atoms in the .gro file,
placing this water in the end.

   For sure one molecule is no problem and I already did it, but if I
had a bunch of systems in this situation ? Is there any trick to make
this automatic ?

Diego Enry

Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.

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