AMBER Archive (2008)

Subject: Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?

From: FyD (
Date: Sat Nov 29 2008 - 01:30:19 CST

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 have been
designed for this task with the corresponding tutorials @

- 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. See project F-1 up to F-44
  * if "central" see
  * if "terminal" see

- 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,
  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

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