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:
http://wiki.gromacs.org/index.php/Parameterization
With special consideration of the fact that the oxygen is probably bound to
heme:
http://wiki.gromacs.org/index.php/Exotic_Species
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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