AMBER Archive (2009)

Subject: Re: [AMBER] atom types

From: David A. Case (
Date: Tue Jan 27 2009 - 09:13:30 CST

On Tue, Jan 27, 2009, deepti nayar wrote:

> I am trying to simulate prot-RNA compolex using ff99SB forcefield. I have
> made the required changes in my pdb file as in:

> 1. I checked for TER between protein and RNA
> 2. changed RNA bases name FROM a/u/g/c to RA/RU/RG/RC
> 3. added 5' and 3' to starting and end base of RNA

> >
> > prot = loadpdb qu2-mod_mod.pdb
> Loading PDB file: ./qu2-mod_mod.pdb
> Enter zPdbReadScan from call depth 0.
> Warning: name change in pdb file residue 0 ;
> this residue is split into RG5 and RG.

This looks like your pdb file doesn't have residue numbers, or doesn't
have them in the correct column.

> Mapped residue G, term: Terminal/beginning, seq. number: 917 to: DG5.
> Mapped residue G, term: Nonterminal, seq. number: 918 to: DG.

This indicates that LEaP did not see the "RG" residue name (for some seems to have done that in the earlier run), so it is
thinking that "G" means "DG".

> Created a new atom named: O2' within residue: .R<DG5 918>

Of course, LEaP is now confused, since there should be no O2' atom in an
RNA residue.

> Joining DG5 - DG
> Created a new atom named: OP1 within residue: .R<DG 919>
> Created a new atom named: OP2 within residue: .R<DG 919>
> Created a new atom named: O2' within residue: .R<DG 919>
> Added missing heavy atom: .R<DG 919>.A<O1P 2>
> Added missing heavy atom: .R<DG 919>.A<O2P 3>

The phosphate oxygens are mislabelled in your pdb file. The
IUPAC/PDB/Amber standard is O1P,O2P, but you pdb file appears to have
OP1, OP2.

If you are not experienced with Amber, I recommend you start with
something a lot simpler than a giant 915-residue protein/RNA complex.
Work first with just a piece of RNA by itself, maybe a small protein by
itself. Once you have some experience under your belt, you will be
better able to tackle this very large system. Remember that you will
have to learn to read error messages and debug things on your own, if
you hope to make any real progress.


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