I see I can change all the His in my protein by that way. But how can I only change one His to double protonated and leave the other single protonated?
On Tue, Jun 7, 2016 at 6:42 AM, Charles Schwieters <[email protected]> wrote: > > 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 > -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis
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