[phenixbb] elbow question
Schubert, Carsten [PRDUS]
CSCHUBER at its.jnj.com
Fri Jun 3 07:10:01 PDT 2011
picking up on that thread: Any plans in the works to add pH dependent protonation to elbow? I don't think this is available yet.
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Nigel Moriarty
> Sent: Thursday, June 02, 2011 2:58 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] elbow question
> There is a bug that adds the hydrogen. I corrected it and generated the
> attached file. The bug fix will be in a future nightly build very soon.
> Note that the hydrogens are not on the phosphates because eLBOW assumes
> a neutral pH. If you want them, I can provide a restraints file
> including them.
> On Thu, Jun 2, 2011 at 7:32 AM, wtempel <wtempel at gmail.com> wrote:
> > Dear colleagues,
> > am I alone in thinking that in my example phenix.elbow gave me more
> > than what I was asking for, specifically atom H11 attached to sulfur?
> > Is it added by elbow, or does it originate from the "--chem=tpp"
> > input?
> > Best regards,
> > Wolfram Tempel
> > command line: phenix.elbow --chem=tpp --mogul phenix version:
> > 1.7.1-743
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division Lawrence Berkeley
> National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709
> Email : NWMoriarty at LBL.gov Fax : 510-486-5909 Web :
More information about the phenixbb