AMBER Archive (2009)

Subject: Re: [AMBER] How to build amide bond etween two protein chains

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jun 24 2009 - 01:18:25 CDT

Dear Jian,

> I have modified protein system that need construct top and crd
> files in xleap. Sidechain (NH2) of non-terminal Lysine in protein A
> form amide with C-terminal (C=O) of protein B, the whole system
> seems like fork or "Y" sharp. In leap, I have tried to directly
> build bond between N atom of Lysine in protein A and C atom in
> protein B, but hydrogen can not match request. How can deal with
> such situation? Built new residue type or any other ideas? Thanks a
> lot.

Your system is like a "cystine". Right ? If so, you need to develop a
new FF library for this connecting lysine.

For that, you could use R.E.D. http://q4md-forcefieldtools.org/RED/

You need a single P2N input file Mol_red1.p2n for your Lysine making
three peptid bonds with three connecting groups:

ACE-NHCHCO-NME NHCHCO
      (CH2)4 --> (CH2)4
       NH-ACE NH

You define three INTRA-MCC for those ACE(1 & 2) and NME chemical
groups during the charge fit:

INTRA-MCC 0.0000 | A1 A2 A3 A4 A5 A6 | Remove
           A1 A2 A3 A4 A5 A6: atom numbers for the ACE(1) chemical group
           R (or Remove): atom H3T removed from the final FF library
(mol2 file)
INTRA-MCC 0.0000 | B1 B2 B3 B4 B5 B6 | Remove
           B1 B2 B3 B4 B5 B6: atom numbers for the ACE(2) chemical group
INTRA-MCC 0.0000 | C1 C2 C3 C4 C5 C6 | Remove
           C1 C2 C3 C4 C5 C6: atom numbers for the NME chemical group

For the definition of INTRA-MCC in P2N input file see:
http://q4md-forcefieldtools.org/Tutorial/

regards, Francois

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