Dear dac,
On Mon, 12 Jul 2004, David A. Case wrote:
> On Mon, Jul 12, 2004, Arvind wrote:
> >
> > i am planning to do a MD simulation of a nucgen generated dodecamer
> > CGCAAAUUUGCG but with a DNA backbone. Is this possible in AMBER?
>
> Yes, but you will need to create a deoxy-U residue. I would recommend
> starting with thymine, and using the "edit" command in LEaP to remove
> the methyl group and replace it with an H. You will either have to run
> RESP to get charges, or hand-merge the uracil charges into your residue.
> Then you can build the molecule you want.
>
> ...good luck...dac
>
i was thinking of hand-merging the uracil charges into my residue. But
this thing is not very clear to me. Supposing i pick up the charges for RU
from the file $AMBERHOME/dat/leap/lib/all_nucleic02.lib (line no.s
6291-6320) but then the backbone wud be having 2 hydrogens (type 'HC')
attached to C2' as in a DNA backbone. So what wud be the charges for these?
These whole thing seems odd because the charges for even the atoms common
to DNA/RNA backbones are completely different for different residues (for
eg. the charges for DT backbone). Once the O2'-HO'2 is changed to H2'2,
won't the whole set of partial charges for all the atoms change?
So what is the correct way of hand-merging the charges?
Or have i misunderstood your suggestion?
--
Regards,
Arvind.
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Received on Wed Jul 14 2004 - 12:53:01 PDT
