VMD-L Mailing List

From: Anna Petroff (abp0006_at_uah.edu)
Date: Thu Mar 15 2018 - 14:31:27 CDT

Thanks, JC!

I'm hoping to get some larger-scale information about the system before I
hope to learn about the finer aspects. Thanks again for your thoughts and
paper!

On Thu, Mar 15, 2018 at 1:48 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> As the group that did the cobalamin parameters, let me *wholeheartedly*
> endorse Josh’s approach *unless* you are interested in the fine details
> of the interactions around the iron as we were with the cobalt.
>
> Best,
> JC
>
>
> On Mar 15, 2018, at 1:21 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
> Hi Anna,
>
> I'd be surprised if there was a ready-made patch for your specific
> situation (at least in CHARMM). When I was looking at a bacterial
> reaction center, which features a non-heme iron coordinated somewhat
> similarly to what you describe (4 HSD + a glutamate), the solution was a
> custom patch (given below) that enforced all the interactions as though
> they were bonds and kept the charge on the iron reasonable. Since bonded
> atoms are excluded from direct electrostatic interaction, this was good
> enough to catch the general electrostatics of the center for distant
> parts of the protein that we were actually studying, and the bonds kept
> the interaction geometry intact so the iron didn't float off. A more
> rigorous approach would be to explicitly parameterize your clusters,
> somewhat like what was done recently for cobalamin
> (10.1021/acs.jctc.7b01236).
>
> -Josh
>
> PRES RCFE 1.00 ! patch for FE2+ in PRC
> ! 2 bonds to COO- terminal of GLU
> ! 4 bonds to unprotonated N of the 4 HIS (HSD)
> ! usage in psfgen (the order must be precisely the following):
> ! patch RCFE HSD230 HSD266 HSD219 HSD190 GLU234 FE
> GROUP !
> ! HSD 1 - atom types !
> ! containing letter W ! 1HE1 2HE1
> ATOM 1CE1 CPW2 0.27 ! | |
> ATOM 1HE1 HR1 0.13 ! --1CE1 2CE1--
> ATOM 1NE2 NRW -0.65 ! || ||
> ATOM 1CD2 CPW1 0.25 ! || ||
> ATOM 1HD2 HR3 0.10 ! \\ || || //
> ! HSD 2 - atom types ! 1HD2-1CD2--1NE2 2NE2--2CD2-2HD2
> ! containing letter X ! \ /
> ATOM 2CE1 CPX2 0.27 ! --3CE1 \ / 4CE2--
> ATOM 2HE1 HR1 0.13 ! / \\ \ / // \
> ATOM 2NE2 NRX -0.65 ! 3HE1 \\ \ + / // 4HE1
> ATOM 2CD2 CPX1 0.25 ! 3NE2----6FE----4NE2
> ATOM 2HD2 HR3 0.10 ! 4HD2 / / + \ \ 4HD2
> ! HSD 3 - atom types ! \ / / \ \ /
> ! containing letter Y ! ==3CD2 / \ 4CD2==
> ATOM 3CE1 CPY2 0.27 ! | |
> ATOM 3HE1 HR1 0.13 ! 5OE1 5OE2(-)
> ATOM 3NE2 NRY -0.65 ! \\ /
> ATOM 3CD2 CPY1 0.25 ! \\ /
> ATOM 3HD2 HR3 0.10 ! 5CD
> ! HSD 4 - atom types ! |
> ! containing letter Z ! |
> ATOM 4CE1 CPZ2 0.27 ! 5HG1-5CG-5HG2
> ATOM 4HE1 HR1 0.13 ! |
> ATOM 4NE2 NRZ -0.65 ! |
> ATOM 4CD2 CPZ1 0.25 !
> ATOM 4HD2 HR3 0.10 !
> ! GLU !
> ATOM 5CG CT2 -0.23 !
> ATOM 5HG1 HA 0.09 !
> ATOM 5HG2 HA 0.09 !
> ATOM 5CD CC 0.75 !
> ATOM 5OE1 OC1 -0.55 !
> ATOM 5OE2 OC2 -0.55 !
> ! !
> GROUP !
> ! FE !
> ATOM 6FE FE 1.00 !
>
> ! patching bonds
> BOND 6FE 1NE2 6FE 2NE2 6FE 3NE2 6FE 4NE2
> BOND 6FE 5OE1 6FE 5OE2
>
> ! patching angles
> ANGLE 6FE 1NE2 1CE1 6FE 1NE2 1CD2
> ANGLE 6FE 2NE2 2CE1 6FE 2NE2 2CD2
> ANGLE 6FE 3NE2 3CE1 6FE 3NE2 3CD2
> ANGLE 6FE 4NE2 4CE1 6FE 4NE2 4CD2
> ANGLE 6FE 5OE1 5CD 6FE 5OE2 5CD
> ANGLE 1NE2 6FE 2NE2 1NE2 6FE 3NE2 1NE2 6FE 5OE1 1NE2 6FE 5OE2
> ANGLE 2NE2 6FE 3NE2 2NE2 6FE 4NE2 2NE2 6FE 5OE1 2NE2 6FE 5OE2
> ANGLE 3NE2 6FE 4NE2 3NE2 6FE 5OE1 3NE2 6FE 5OE2
> ANGLE 4NE2 6FE 1NE2 4NE2 6FE 5OE1 4NE2 6FE 5OE2
> ANGLE 5OE1 6FE 5OE2
>
>
> On 03/15/2018 10:28 AM, Anna Petroff wrote:
>
> Hello,
>
> I'm seeking recommendations on how to identify non-heme coordinations
> between iron and His in VMD/NAMD. From what I've read, there are some
> nice patch options for heme coordination, but I haven't found one
> specific to non-heme coordination. Is there a best-practice way to
> handle this situation?
>
> My protein of interest has a diiron active site. One of the irons is
> coordinated with five histidine residues (all HSE). The other iron is
> coordinated with four histidines (also all HSE), as well as an
> interaction with a glutamine residue that is mediated by a water
> molecule.
>
> I would like to set these coordinations in NAMD2, possibly through a
> combination of patches. If you have experience related to this type of
> problem, I'd really appreciate your thoughts.
>
> Thanks for your time,
> Anna
>
>
>
>
>