Hi Pragya,
You can use a visualization program such as GaussView to do that.
-Pengfei
> On Feb 3, 2020, at 11:39 PM, PRAGYA PRIYADARSHINI <pragya.imtech.res.in> wrote:
>
> Hello,
> I am generating parameter for oxy-heme B (having net charge zero) using mcpb in AMBER.
>
>
> When using reduce command to add hydrogen, it is adding hydrogen to the whole molecule except the propionate group. To make the whole molecule charge neutral I need to add hydrogen on propionate.
>
> Kindly suggest how to do it
>
>
>
>
> Best Regards
>
>
>
>
> Pragya Priyadarshini
>
> Bioinformatics Center
>
> CSIR-IMTECH
>
> Chandigarh, INDIA
>
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Received on Fri Mar 27 2020 - 14:00:02 PDT
