On Thu, Jun 13, 2019, Alessandro LANDI wrote:
>
>After generating a pdb for a short DNA sequence (say GTG) with the 'fiber'
>command of 3DNA, I used Molden to convert it to xyz format and to add the
>missing hydrogens. Then I have added Na+ ions to achieve neutrality and
What version of AmberTools are you using. Recent versions should(?)
complain that antchamber is for organic molecules only, and doesn't
handle Na+ ions. The RESP charges for standard nucleotides were
generated from anions, not constructs neutralize with Na+, so that
might be the best way to proceed.
>
>"Na 0.000 0.000 ATTN, need revision"
>"h5-na-cc-nd 1.1 180.0 2.0 Using default
>value"
Clearly antechamber has gone wrong here, thinking that sodium has
chemical bonds to other atoms. So, try removing your sodium ions.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 15 2019 - 06:00:02 PDT
