Re: AMBER: RNA sequence with DNA backbone?

From: Vlad Cojocaru <>
Date: Wed, 14 Jul 2004 13:09:13 +0200

Dear Arvind,
  You can try to take the charges of the base from the RNA residue and
the charges of the sugar from the DNA residue (excluding N1 atom). At
the end try to adjust the N1 charge so that the total charge will be -1.
It should give you reasonable charges.

Arvind wrote:

>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?

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Wed Jul 14 2004 - 12:53:01 PDT
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