[gmx-users] heme and TML
David van der Spoel
spoel at xray.bmc.uu.se
Wed Feb 13 21:46:52 CET 2002
On Wed, 13 Feb 2002, Patricia Soto wrote:
>1. For the HEME parameters we have in gromacs, which is the oxidation
>state of Fe?
It's not that fancy I'm afraid. Of course you could count the net charge
on the HEME group... That is why ligated residues are just treated as
>2. Does anybody have the topology for tri-methylated lysine?
I don't but it is really easy to make! Assuming you will use united atoms
for the CH3 groups, you edit the LYS entry in the rtp file, replace the
HZ1-3 by CH3, and adjusted the charges and the bond length. Charges you
can probably "borrow" from lipid topologies. You also have to update the
corresponding hdb file and copy the entry for LYS to TML, and take away
the entry that generates the hydrogens on the NZ.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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