AMBER Archive (2009)

Subject: Re: [AMBER] branched aminoacids

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Dec 17 2009 - 03:49:16 CST

Alessandro,

> I'd like to derive a parameter file for an unnatural aminoacid having
> one amino head and two carboxy tails, but I have a couple of questions.
> First of all, is this possible with amber? How do I define the two
> carboxy tails in the off file?

If you look at the cystine (not cysteine) residue: CYX in the Amber
Force Field Topology DataBase I think you get an example of what you
need.

xleap -f leaprc.ff99SB

desc CYX
> desc CYX
UNIT name: CYX
Head atom: .R<CYX 1>.A<N 1>
Tail atom: .R<CYX 1>.A<C 9>
Contents:
R<CYX 1>
> desc CYX.1
RESIDUE name: CYX
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 0
Type: protein
Connection atoms:
  Connect atom 0: A<N 1>
  Connect atom 1: A<C 9>
  Connect atom 2: A<SG 8>

  => connect0, connect1 & connect2 are defined

> Is it possible to use a standard version
> of REDIII for deriving RESP charges?

With R.E.D.-III.3, you will be able to derive the N-terminal,
C-terminal and Central fragments in three different jobs. With R.E.D.
Server/R.E.D.-IV all can be done in a single step.

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24 for the
global strategy for the three different fragments.

- If we only discuss about the central fragment:
   I think you need a fragment like:

  NH-CH-CO
     R with R = R'CO

to get this fragment, you could use the following 'whole' molecule:
  ACE-AA*-NME
      R with R = R'CO-NME

This means you simply use 3 intra-molecular charge constraints
(INTRA-MCC keyword) in the corresponding P2N file (for ACE & 2 NMEs)
and the job is done...

You follow exactly the same strategy for the N-terminal & C-terminal
fragments using Methylammonium & Acetate - but here you will have to
replace one intra-molecular charge constraint by one inter-molecular
charge constraint (INTER-MCC keyword). Once again this is
straightforward...

regards, Francois

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