Dear sir:
I have followed your suggestions and define a new residue for the lysine
and carboxyl that are being joined. When I load the tleap and save the
inpcrd and prmtop files, it seems Ok, but when I change the inpcrd to pdb, I
found that the new residues have a TER mark between the other residues.
Thus, when I perform the minimization, the new residue will move apart from
the other parts of the molecule.
How do I connect the new residue to the other parts of the molecule? (
there are three connecting points, one in the terminal of one part, and two
in the another)
Thank you!
Best Regards!
Your sincerely:
Zhou Gong
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Biomolecular Physics and Modeling Group
Department of Physics
Huazhong University of Science and Technology Wuhan 430074, Hubei China
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·¢¼þÈË: case [mailto:case.biomaps.rutgers.edu]
·¢ËÍʱ¼ä: 2012Äê5ÔÂ6ÈÕ 19:49
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] ´ð¸´: ´ð¸´: add H-atoms automatic in tleap
On Sun, May 06, 2012, Zhou Gong wrote:
> The way you said such as redistribute the residual charge, or use
> RESP, and change the atoms types of N atoms. Are these operation can
> be done in the Xleap?
You can change atom types and charges in LEaP; easiest way is to select a
set of atoms, and use the "edit selected atoms" menu item.
> If I couldn't done these in Xleap, next time, when I load the pdb
> file into the leap, it will add the extra H-atoms again.
This is true: you have to get everything done in one pass. Alternative is
to define new residues for the lysine and carboxyl that are being joined.
You have a situation which is not a standard one, and you will have to
experiment some, and learn a lot of new techniques. You might want to start
with just two residues for such experiments.
....dac
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Received on Sun May 06 2012 - 08:00:03 PDT
