[gmx-users] atomtype OW is not found

[Justin Lemkul]

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"
> #ifdef POSRES_WATER
> ; 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

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

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