AMBER Archive (2004)

Subject: Re: AMBER: Residue Loading Problem

From: David A. Case (
Date: Thu Dec 16 2004 - 20:10:43 CST

On Fri, Dec 03, 2004, Garhan Attebury wrote:

> I've recently started to resurrect an old project using Amber...

> CF.lib - The Fluorescein atoms are of residue type CF, and since that's
> the name of this file I'm assuming this describes them in some way. I
> am confused as to the purpose of the .lib files. I realize you
> generate/load with loadOff and saveOff in leap but how do they relate to
> the above dcf.prep and parm99-2.dat? Are these libraries basically all
> the "changes" that the above two files do to your overall molecule?

You may need to use loadOff with this file *before* reading in the pdb
file that has fluorescein in it. Try doing this instead of reading in the
dcf.prep file: given the messages you got, it's certainly possible that
dcf.prep is not in sync with the pdb file, but that CF.lib is.

> So, with the above files I do the following...
> > loadamberprep dcf.prep
> Loading Prep file: ./dcf.prep
> > loadamberparams parm99-2.dat
> Loading parameters: ./parm99-2.dat
> > ml2f = loadpdb ml2f.pdb
> Loading PDB file: ./ml2f.pdb
> Created a new atom named: C within residue: .R<CF 14>
> Created a new atom named: 6O1 within residue: .R<CF 14>
> Added missing heavy atom: .R<CF 14>.A<16O 72>
> Added missing heavy atom: .R<CF 14>.A<5C 40>
> total atoms in file: 952
> Leap added 2 missing atoms according to residue templates:
> 2 Heavy
> The file contained 2 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
> Looking at the molecule, I see the two added atoms are not even supposed
> to be there (they really are extra) and are seriously close to existing
> ones.

This needs to be fixed before you continue. If the CF.lib won't help, you
may want to create a fluorescein-only pdb file and feed it to antechamber.

Sorry to be so slow in replying...hope this helps.....dac

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