AMBER Archive (2009)

Subject: Re: [AMBER] branched aminoacids

From: Alessandro Contini (alessandro.contini_at_unimi.it)
Date: Thu Dec 17 2009 - 05:22:56 CST

Dear Francois,
thank you for the detailed directions, it was exactly what I needed.

Best regards,

Alessandro

Il giorno gio, 17/12/2009 alle 10.49 +0100, FyD ha scritto:
> 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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