AMBER Archive (2009)

Subject: Re: [AMBER] making leap to recognize 5' phosphate

From: FyD (
Date: Wed Jun 24 2009 - 01:02:42 CDT

Dear Bala,

> Thank you for the information. I have attached the pdb of my complex. In
> the attached pdb, residue 1 which is Adenine has a free 5' phosphate. I want
> to consider this phosphate during simulation. When i see DA5 or RA5 residue
> in xleap, it dosent have the phosphate. Now i have find a way to consider
> the phosphate explicitly. Kindly write me if there is any easy way to create
> such residue and load it in xleap.

If I understood your structure you have a 5'-terminal phosphate for a
pentanucleotide and you have no connection between your protein and
your nucleic acid structure.

In the Amber FF topology database (FFTopDB), the terminal residues are
3'OH & 5'OH and the total charge of those residues are -0.6931 and
-0.3079, respectively. Consequently, I think the best approach is to
develop two new FF libraries: one for the connecting nucleoside and
the other for the 5'-phosphate.

I suggest you to use R.E.D. for that:
The molecule 1: you could start from Methylphosphate (-2) & see how it goes
The molecule 2: your connecting nucleo_side_

In the P2Ns (Mol_red1.p2n & Mol-red2.p2n) you define:
- an INTRA-MCC for the H3T atom of molecule 2 sets to the charge value
of H3T in the Amber FFTopDB
           X.XXXX = value of the constraint = 0.4396
           A: atom number in the P2N file for H3T
           R (or Remove): atom H3T removed from the final FF library
(mol2 file)
- an INTER-MCC between the methyl group of methylphosphate & the HO5'
hydroxyl (defined in molecule 1).
INTER-MCC 0.0000 | 1 2 | A1 A2 A3 A4 | B1 B2
           A1 A2 A3 A4 atom numbers of methyl group (in the P2N file;
molecule 1)
           B1 B2 atom numbers of HO5' hydroxyl (in the P2N file; molecule 2)

You should get what you need: Look at the RRMS value of the fit in the
"Mol_MM" directory.

For the use of INTR-MCC & INTER-MCC in R.E.D. see

At the end, you might need to follow:
to make your FF library more "presentable"

regards, Francois

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