Hello Jitrayut,
> But how to delete HG and bond the atom C1 and OG after load
> the following pdb file in tleap. Do you know how to do that ? (REMOVE and
> BOND ?)
You need to create your own FF library(ies) for (a) molecular
fragment(s) corresponding to your protected Serine(s?).
The R.E.D. tools
http://q4md-forcefieldtools.org/RED/ have been
designed for this task with the corresponding tutorials .
http://q4md-forcefieldtools.org/Tutorial/
- You need to know if your protected Serine is "central" or "terminal"
in your peptide chain.
You will find many examples of such fragments in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/ See project F-1 up to F-44
* if "central" see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
* if "terminal" see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11
- You need to know for which FF this/these new FF library(ies) are designed ?
This means what is the theory level used in the MEP computation step ?
HF/6-31G* in vacuo or B3LYP/cc-pVTZ in Ether.
- You need to decide which conformation(s) you want to select for your
new residue.
This is well explained . Cieplak et al. J. Comput. Chem., 1995, 16,
1357-1377.
This is the reference in this type of work.
- If you want to get reproducible charge values you will have to
control the molecular orientation of your optimized geometry. So far,
this can be only achieved using the rigid-body re-orientation
algorithm available in R.E.D.
- Finally, you might be interested to derive new FF library for
protected Serines with various chemical groups used in peptide
synthesis, i.e. not only for your Acetyl-serine... For this, splitting
your protected Serine into two parts would be the best choice, with a
non-various part i.e. Serine with side chain = CH2-O and with a
various part P being your different protective groups.
Do not hesitate to ask if you have questions: All this represents a
real work by itself...
I hope this helps,
regards, Francois
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 18:08:16 PST
