[gmx-users] Error in running energy minimization

Rahma Dahmani rahma.dahmani at fst.utm.tn
Fri Nov 9 09:53:42 CET 2018

Hi GMX users,

I am running energy minimization for my ligand in water box ,
I have manually constructed a topology file for my ligand (with antechamber
tools) and i introduced all the necessary atomtypes, even for water
molecules ( i created *itp file*, named water.itp,  where i include the
defintions of  water atom types and all their necessary parameters like in
tip3p.itp water model in amber ) but unfortunately when i used 'grompp'
command to run energy minimization it* didn't recognize OW atom type , *when
i replaced atom-Type, inside itp file, by *oh *which is not correct to
describe water oxygen atoms but it worked for energy minimization and *the
job run normally* ....which is weird since in amber atom type OW (water) is
different from OH (hydroxyl) atomtype.

please find enclosed my water.itp file with modified water atomtype (oh,
ho, ho), where i used amber water parameters for tip3p model.

and my questions are *:* why 'grompp' didin't recognize OW atomtype even if
i already included all the necessary definitions of atomtypes ? and Is it
OK to use hydroxyl atomtype to describe water atoms ?

Can you help me please,
Thank you !

*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*

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