[gmx-users] atomtype OW is not found

Justin Lemkul jalemkul at vt.edu
Wed Nov 7 16:10:51 CET 2018

On 11/7/18 9:48 AM, Rahma Dahmani wrote:
> Hi Gromacs users,
> I used antechamber tools to genrate a topology and coordinates files for my
> ligand, then i used acpype to convert them to gromacs files (.top and
> .gro), then *i added manually water FF in topology file* since i want to
> run MD simulation of ligand in water ....
> I double checked the notation of water molecule (OW and HW) in gro file
> ....but i always get this error  """ *atomtype OW is not found* """"

Coordinate files contain atom *names*, not atom *types.*

> here I copy paste a part of my topology file where i include water FF
> ; Include water topology
> #include "amber99sb-ildn.ff/tip3p.itp"
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif

If you're manually constructing a topology, you need to introduce all 
the necessary atom types. The tip3p.itp topology assumes that the water 
atom types (and associated parameters) have already be read from a 
parent force field. If you only have a ligand topology and water 
topology in your system .top, then you will be missing the definitions 
of the water atom types.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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