AMBER: Residue Loading Problem

From: Garhan Attebury <>
Date: Fri, 03 Dec 2004 00:20:51 -0600

I've recently started to resurrect an old project using Amber for the
Chemistry department at my university. In particular, I'm trying to
simulate a DNA 14-mer with a Fluorescein dye attached at one end. My
current problems arise from the fact that this project hasn't been
worked on in over three years and those who were once involved and are
still around don't remember much of what went on. Problems further
arise from the fact that I don't know if I have all the files previously
used in the project.

My main issue is that of either loading and using the residues which
were previously created or creating new ones from scratch. Also, the
previous project used Amber 6 and I am now using Amber 8. I realize
there are some format incompatibilities between the different versions.
  Anyway, The files I have include the following...

ml2f.pdb - This is the PDB of the 14-mer with the Fluorescein attached.
  I've loaded it up in VMD and everything looks as it should. xleap of
course complains about the atoms not in residue templates (more on this

dcf.prep - This is the exact same file format as the two residue input
files in the plastocyanin tutorial.

parm99-2.dat - This appears to be a copy of the parm99.dat that ships
with amber, but with modifications added by the person who started this
project (some lines were commented with their name). The plastocyanin
tutorial mentions creating an frcmod file instead of modifying the main
force field file directly but that's apparently not what was done.

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?

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. Removing them for the heck of it (I know something is "wrong" by
this point) and checking the overall charge of the molecule indicates
that the charge isn't an integral value. I've looked closer and the
charges on the Fluorescein are the culprit (the main 14-mer is fine).
This leads me to believe that I'm either (a)mis-interpreting how to
load/use the residues, (b)the two "extra" atoms are a result of
incorrect names and the incorrect names are in the end giving atoms
incorrect charges, or (c)that the residue files themselves are
incorrect/incomplete. I've been told that the previous student had
actually done a MD simulation with the Fluorescein attached, so I'm
leaning towards (b) as my problem.

If anyone has some time to kill or is itching for some problem solving,
I've put up the files mentioned above so you can get at them. (all four above files)

I'm a bit stuck at this point and have started looking into creating
residues from scratch in the event I'm unable to use the old ones.
Still, I'd appreciate it if anyone can point me in the right direction
here. Thanks!

- Garhan Attebury

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Received on Fri Dec 03 2004 - 06:53:00 PST
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