Hi Qinhong,
Following my earlier example:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
import psfGen
psfGen.seqToPSF('myprotein.seq', deprotonateHIS=False) # myprotein.seq is the
name of the file with your sequence
xplor.simulation.deleteAtoms('resid 76 and name HD1') # e.g., delete HD1 from
residue 76
xplor.command('write structure output=myprotein.psf end') # if you want to keep
the psf file for reuse
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Best regards,
Guillermo
________________________________________
From: Val Yu [[email protected]]
Sent: Thursday, July 07, 2016 2:07 AM
To: Charles Schwieters
Cc: [email protected]
Subject: Re: [Xplor-nih] About histidine protonation state
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]<mailto:[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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