AMBER Archive (2006)

Subject: Re: AMBER: Using modified NA bases

From: Franck_Vendeix_at_ncsu.edu
Date: Tue Oct 24 2006 - 08:03:36 CDT

Hi Fabian,

You could check the following website:
http://ozone3.chem.wayne.edu:8080/Modifieds/index.jsp. This website
contains a list of modified bases with their corresponding AMBER ff
parameters and charges.
You could also use R.E.D ( http://www.u-picardie.fr/labo/lbpd/RED/) which
is a useful software for the calculation of partial charges.

Cheers,

Franck

> Seth,
> I use modified DNA, and this is more o less my script to be used with
> tleap (tleap -s -f leap.in when leap.in 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
> quit
>
>
> 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?
>
>
> cheers,
> fabian rodriguez.
>
>
> cheers,
> far
>
>
> On Mon, 2006-10-23 at 15:59 -0400, sethl_at_gatech.edu 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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