[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
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
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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