AMBER Archive (2006)

Subject: RE: AMBER: change atom in a DNA double strand

From: Carra, Claudio \(JSC-SK\)[USRA] (
Date: Mon Jul 10 2006 - 14:24:02 CDT

Hi David,
thanks a lot for your answer.
I've basically tried 2 methods. the initial procedure is common:

I've generated the sequence of DNS with nucgen, I've add all the
I've copied the pdb part of the guanine I wanted to alter. I've
optimized the fragment, freezing the coordinates of the sugar and PO4-,
by b3lyp/6-31g* Now that we got the geometry in the right orientation
I've used 2 different method

1. the one very similar to the tutorial but it is not really working
because I got an error in the unit.
normally this can be fixed by using parmchek on the .prep file.
in the tutorial u use a frcmod file but I'm not sure to have understood
u get that. that's the keypoint, otherwise I can't save the topology
anyway, I've calculated the charges from the modified guanine, single
point on all the unit, HF/6-31g*, by resp fitting on mk population
analysis, with antechamber. From the resp file, loaded with xleap, I can
see that new set of charges and copy them in the previous pdb file to
which I've added manually the bonds, as in the tutorial. in this way I
can have the new set
of charges in the correct orientation. I adjust tail and head, but when
I check the new residue I got
"could not find angle parameter : ..." for several atom.

I'm not surprised, I never put it.

if, from the previous prep used to generate the atom charges, I use the
corresponding frcmod file, generated with parmcheck, and I load it in
I got a similar error probably due to the different atom orientation
from the initial pdb and final prep file.

2. In the same geometry, I've recalculated the charges, assuming that
the total charge is -1.
I've used anthechamber to generate the resp file, and parmchek for the
extra torsional parameters. All perfect, the new residue is ok, however
the orientation and the order of atom of the molecule in the bdb from
the resp file is different, so atoms in the bdp file don't result bonded

hope my mail was not too confusing
thanks a lot in advance for your help

> I'd would like to modify an atom of residue in a DNA double strand.
> The initial geometry from the canonical structure generated by
> nucgen is absolutely fine, but than, I'd like to have a guanine in
> the middle of the double strand replaced the corresponding oxidized
> it is easy to generate a new library with antechamber for a small
> but I didn't find any example where a new molecule (not atom) is
> into a macro system.
> The error I get and I can't fix is relative to missing parameters
> for the force field, which in general can be fixed by loading frcmod
> file, but not in this case.

Why does it not work "in this case"? What is the error message? Please
to give details about exactly what you tried, and what the result was.

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