AMBER Archive (2009)

Subject: Re: [AMBER] four prepin/frcmod files be read simultaneously by leap

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jan 07 2009 - 12:39:56 CST

On Wed, Jan 07, 2009, Yi Mao wrote:

> > 2d1s = loadPdb a.pdb
> Loading PDB file: ./a.pdb
> -- residue 28: duplicate [ CD] atoms (total 2)
> -- residue 28: duplicate [ CG] atoms (total 2)
> -- residue 28: duplicate [ NE2] atoms (total 2)
> -- residue 28: duplicate [ OE1] atoms (total 2)
> -- residue 354: duplicate [ CG2] atoms (total 2)
> -- residue 354: duplicate [ OG1] atoms (total 2)
> -- residue 233: duplicate [ CG1] atoms (total 2)
> -- residue 233: duplicate [ CG2] atoms (total 2)
>
> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> (same-name atoms are reduced to a single atom)

You need to check on the above, and remove the duplicate names!
>
> Added missing heavy atom: .R<LYS 15>.A<CD 11>
> Added missing heavy atom: .R<LYS 15>.A<CE 14>
> Added missing heavy atom: .R<LYS 15>.A<NZ 17>

...etc

Above might or might not be OK...check to see what atoms are indeed
missing from your pdb file. Be sure to check that LEaP built them in
reasonable positions.

>
> So my question is still why adding one more ligand won't work with leap?

This may have nothing to do with the number of ligands--see below.

> >> Could not find angle parameter: ca - ne - c
> >> Could not find angle parameter: ca - ne - cf
> >> Could not find angle parameter: nb - ca - ne
> >> Could not find angle parameter: na - ca - ne
> >> Building proper torsion parameters.
> >> ** No torsion terms for ca-ne-cf-ss
> >> ** No torsion terms for ca-ne-cf-cd

You need to examine your frmcmod files to see if/why these are missing.
Did you run parmchk for both ligands? Anyway, the error messages are
really quite specific, so you should be able to track down what is
missing.

...dac

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