AMBER Archive (2006)

Subject: Re: AMBER: Using modified NA bases

From: Fabian Alejandro Rodriguez (
Date: Mon Oct 23 2006 - 18:17:41 CDT

I use modified DNA, and this is more o less my script to be used with
tleap (tleap -s -f when is the following):

mods = loadamberparams gux.frcmod
loadamberprep gux.prepin
set GUX head GUX.1.P
set GUX tail GUX.1.O3'
bdna = loadpdb 14R.full.initial.pdb
saveamberparm bdna 14RfullBdnaInt.vac.prmtop 14RfullBdnaInt.vac.prmcrd
addions bdna Na+ 0
solvateoct bdna TIP3PBOX 8.0
saveamberparm bdna 14RfullBdnaInt.wat.prmtop 14RfullBdnaInt.wat.prmcrd

gux = modified guanine base
do you understand what I do?
It works for me.
basically, I have a prepin file with only the modified base and I load
it, then I set the head and tail atoms (linkage point to other bases)
and then I load the full pdb file (DNA + modified base)
if you look the results in xleap, i.e., edit bdna (in my example) you'll
see that the modified base in incorporated in the DNA.

One question from me to you in particular, how do you calculate the
partial charges for your modified bases?

fabian rodriguez.


On Mon, 2006-10-23 at 15:59 -0400, wrote:
> Dear Amber Community,
> I would like to know the most common way to go about building nucleic acid
> complexes with custom/modified bases. Right now I have generated a library of
> prep files that contain my modified bases but then how would I go about
> constructing a structure file for a helicoidal duplex using these bases?
> Thanks,
> Seth
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