[phenixbb] elbow question

[Nigel Moriarty]

Carsten

There are three levels of pH dependance in eLBOW at the moment. From the

phenix.elbow --help

--pH=PH               specify --pH=low to retain exact input chemistry
                        --pH=neutral to remove hydrogens from acids ...
                        --pH=high to add hydrogens to amines

Neutral pH (the default) also removes hydrogens from phosphates.

If you are referring to in situ pH calculations, its on the list.

Nigel


On Fri, Jun 3, 2011 at 7:10 AM, Schubert, Carsten [PRDUS]
<CSCHUBER at its.jnj.com> wrote:
> Hi Nigel,
>
> 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.
>
> Thoughts?
>
> Cheers,
>
>        Carsten
>
>
>> -----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
>>
>> Wolfram
>>
>> 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.
>>
>> Thanks
>>
>> Nigel
>>
>> 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  :
>> CCI.LBL.gov
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-- 
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  : CCI.LBL.gov