AMBER Archive (2006)

Subject: Re: Fwd: AMBER: How to build N-terminal of alanine : NH2

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Jun 09 2006 - 01:45:27 CDT

Quoting jitrayut jitonnom <jitrayut.018_at_gmail.com>:

> Thank for your advise but I am new for R.E.DD.B so please give me an idea to
> do. Now I already download file (F-40). By the way, I want to do leap with
> the N-terminal (neutral fragment :F-40) so what I should do next ?

A) Here is a scheme which explains how to proceed using 2 molecules

                 ACE-AA-NME
  NH2Me CH3CO-NHCHRCO-NHMe => NH2CHRCO
     --------------- ----
          (1) (2)
(1) Atoms involved in an inter-molecular charge constraint (set to 0)
(2) Atoms involved in an intra-molecular charge constraint (set to 0)

You could use two conformations for your dipeptide ACE-AA-NME...

B) You might consider a strategy based on a single molecule such as:

  NH2CHRCO-NHMe => NH2CHRCO
           ----
           (2)
(2) Atoms involved in an intra-molecular charge constraint (set to 0)

With R.E.D. you get a mol2 file (force field independent) which can be directly
loaded into LEaP to generate an OFF library (force field dependent with
connection information for molecular fragment). See, for instance the LEaP
script provided with the F-19 R.E.DD.B. project such as:
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-19/script1.ff

For the 'NH2-terminal neutral fragment' of the AIB residue, below are LEaP
commands to use to convert a Tripos mol2 file into an OFF library.

N0AI = loadmol2 N0AI.mol2
set N0AI name "N0AI"
# head = null
set N0AI tail N0AI.1.C
set N0AI.1 connect0 N0AI.1.N
set N0AI.1 connect1 N0AI.1.C
set N0AI.1 restype protein
set N0AI.1 name "N0AI"
# set FF atom types
set N0AI.1.N type N3
set N0AI.1.H1 type H
set N0AI.1.H2 type H
set N0AI.1.C type C
set N0AI.1.O type O
set N0AI.1.CA type CT
set N0AI.1.CB1 type CT
set N0AI.1.HB11 type HC
set N0AI.1.HB12 type HC
set N0AI.1.HB13 type HC
set N0AI.1.CB2 type CT
set N0AI.1.HB21 type HC
set N0AI.1.HB22 type HC
set N0AI.1.HB23 type HC
# save the OFF library
saveoff N0AI N0AI.off

regards, Francois

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