On Wed, Feb 21, 2018, Nikolay N. Kuzmich wrote:
>
> The DNA molecule has the phosphate groups on its 5' ends.
> And I suspect that non-integral charge originates from that.
> The OHE residue was created accordingly.
> This is how one 5'-end looks like:
You don't say what version of Amber you are using, or what commands you
gave to tleap. But the following works for me:
1. Change the atom names in the OHE residue in the pdb file to OP3 and HOP3,
to match the PDB standard.
2. source both leaprc.RNA.OL3 and leaprc.DNA.OL5 (or bsc1). (The OHE
residue is only in the RNA library; cc-ing to Tom Cheatham for advice
on what the best thing to do here is.
3. load the pdb file into tleap and call saveAmberParm. This gives
a charge of -1.0002, which is close enough to -1 for government work.
Note that you will need AmberTools17.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 21 2018 - 05:00:02 PST
