On Wed, Nov 21, 2007, Boutheïna Kerkeni wrote:
>
> 1)The first problem I encountered is that my newly created pdb from
> frcmod file, when visualzed in VMD is completely disconnected no
> bonds between atoms! Is this normal?
VMD uses distance heuristics to decide if there is a bond. Since it doesn't
know anything about iron sulfur bonds, it doesn't draw them. If I use the pdb
file you included in VMD, I see S-C bonds (as I expect), so it is not
"completely disconnected". Not sure what you are seeing.
If you load your off file into xleap, and view it there, you should see the
bonds.
> 2) The second being: how to connect the CB(CT) carbons to CA (ie the
> rest of the 4 CYS of this cubane)??
Use the bond command in LEaP to do this. Note that you will have to define a
special CYS residue that only has the backbone atoms, and use this in place of
the "regular" CYS residues--otherwise, you would have two copies of the SG and
CB atoms.
[We are also working on FeS cubane parameters; we chose to make the "cut"
between the CYS SG and the Fe4S4 cluster, but I don't see much to argue one
way or the other. Send me private email if you are interested. We've done a
some force constant optimization, but not are not finished with that step.]
...regards...dave case
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Received on Sun Nov 25 2007 - 06:07:11 PST
