[gmx-users] Atomtype OWT3 not found during EM step

Justin Lemkul jalemkul at vt.edu
Wed Jul 3 20:46:20 CEST 2013

On 7/3/13 12:46 PM, juganta wrote:
> Dear all,
> I am a new user of GOMACS. My system contains Polymer and Water. I used
> gromos53a6 force field and spc water model, it ran nicely.
> But now I want to use TIP3P water model with the same force field
> (gromos53a6), in that case, I am getting a error message from the 'grompp'
> during energy minimization step - "Fatal error: Atomtype OWT3 not found".
>>From GMX users Forum I got some information to resolve this problem. Such
> that, I added OWT3 at the bottom of the  .atp file of the related force
> field and also edited the nonbonded.itp file. But I couldn't get rid of such
> kind of error.

It would be helpful to see what you actually did.  The .atp file is only used by 
pdb2gmx, so unless you're using pdb2gmx to make a water topology (usually not 
the case), it has no effect.  Editing ffnonbonded.itp is what you need to do, 
but if the modification you made was correct, then there would not be a fatal error.

The bigger point to all of this is that Gromos96 force fields don't provide 
native support for the TIP*P models because they weren't calibrated against 
them.  Gromos96 was balanced against SPC, so one could make the argument that 
the water model is as much a part of the force field requirements as anything 
else.  Proceed carefully, and be prepared to defend your choices.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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