Hello,
I'm forwarding this email to the amber list, which is generally where
these questions should be directed. If you aren't already subscribed
to the list, you can subscribe by sending a blank email to
amber-subscribe.ambermd.org.
To answer the question, make sure that there's no H-atom in the
structure file you're using (PDB i'm guessing?). This is likely to
already be true if you're using a crystal structure. You have to
change CYS to CYX in the PDB file for every atom of the affected
residues. If you do this, xleap should not confused-ly put a H atom
bonded to the S of any CYX residue. However, to actually form the
disulfide bond, you'll have to use the "bond" command detailed in the
AmberTools manual.
An alternative is to use sleap, which will form S-S bonds
automatically according to some cutoff (for which the default is
typically acceptable).
I hope this helps,
Jason
On Thu, Feb 25, 2010 at 9:24 PM, Winnie C <winniec555.gmail.com> wrote:
> Hi Dr. Jason,
>
> After I changed CYS to CYX, I saw undesired H bonded to CYX. How can I
> remove these H-atoms from cysteine disulfide bridges? I am using AMBER 9 and
> xleap.
>
> Shi
> --
> "Hold a true friend with both your hands". -Nigerian Proverb-
> "If you don't have a dream, how are you going to make a dream come true?"
> -Oscar Hammerstein-
>
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 25 2010 - 19:00:03 PST
