[gmx-users] OXY not found

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 5 19:32:22 CET 2009

Andy Torres wrote:
> Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on 
> myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got 
> the following
> Fatal error:
> Residue 'OXY' not found in residue topology database
> I check the ff and I did not found the oxigen molecule.
> I saw that somebody allready use this molecule in the mailing list:
> On Tue, 18 Jun 2002, Valentin Gogonea
> Is there a chance to contact him?

If this individual still subscribes to this list after all these years, you may 
get a reply.

> Is this molecule in any other ff?

Not typically.  The force fields included in Gromacs are generally designed for 
condensed-phase species like proteins, nucleic acids, and small organics.

> How can I fix this?

That depends on your definition of "fix."  If you need to simulate myoglobin 
with oxygen bound, you may be in for the difficult (read: very advanced!) topic 
of parameterization:


With special consideration of the fact that the oxygen is probably bound to heme:


> How can I take the OXI and SO4 molecules out of my .pdb file without 
> making mistakes?

That depends on your definition of "mistake."  Whether or not these molecules 
are relevant to your dynamics is a decision only you can make.


> Hopping to be clear.
> Thanks in advance
> Andy
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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