Hello Qinhong--
> >
> > It seems the default histidine in Xplor-NIH is double
> > protonated. However, all the histidine in my calculated structure is
> > single protonated. Anyway, how to change his protonated state?
> >
>
> Bermejo, Guillermo (NIH/CIT) [E] wrote:
> Hi
>
> If you are using the psfGen.seqToPSF() function to generate the PSF
> file from the sequence, you should change the default value of the
> deprotonateHIS argument to False. For example,
>
> import psfGen
> psfGen.seqToPSF('protein.seq', deprotonateHIS=False) # protein.seq is the
> name of the file with your sequence
>
> I hope this helps.
>
Additionally, you could use the seq2psf helper with the -protonateHIS
argument. As suggested by these responses, you will want to use a PSF
file as long as you need the HIS HD1 atom.
best regards--
Charles
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