[gmx-users] Error in running energy minimization

Jissy Kuriappan jissyakkara at gmail.com
Fri Nov 9 10:22:05 CET 2018

Hi Rahma,

   Did you check the list of atomtypes? It would have the atomtypes defined
for the forcefield you are using (hence has oh), but you have to add the
atomtype OW and HW in your atomtype list. Just adding the itp file wont be
enough?? Hope this helps.

On Fri, Nov 9, 2018, 9:54 AM Rahma Dahmani <rahma.dahmani at fst.utm.tn wrote:

> 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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