[modeller_usage] Histidine protonation state with allhmodel

[Jean Didier Pie Marechal <>]

Dear All,
I am building a model with a specific zinc coordination sphere. I decided to use a full atom run and this actually improved the overall quality of the models.
I have a problem though.  In the structure, the zinc is chelated by several histidines some by  delta others by epsilon chelating modes. However, the resulting models are always with the same protonation state (epsilon). This leads to undesired clashes. How can I stipulate modeller to use a given protonation state with the charmm force field. Should I use the charmm residue code in the initial pdb? Or should I define this in the python script.
Thanks for any help

Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: 

----- Missatge original -----
De: 
Data: Divendres, Febrer 20, 2009 4:02 pm
Assumpte: modeller_usage Digest, Vol 8, Issue 12

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> Today's Topics:
> 
>   1. Academic and Commercial (salam pradeep)
>   2. Re: Academic and Commercial (Modeller Caretaker)
>   3. Using modeller with a web form: how topass the	provided key
>      to modeller? (St?phane T?letch?a)
> 
> 
> --------------------------------------------------------------------
> --
> 
> Message: 1
> Date: Wed, 18 Feb 2009 15:12:48 +0530
> From: salam pradeep <>
> Subject: [modeller_usage] Academic and Commercial
> To: 
> Message-ID:
> 	<>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Is there any variation in the models generated by the Academic 
> version and
> the Commercial version of Modeller.
> Some people say that the Modeller Academic version is not so 
> accurate in
> generating the 3D models.
> How far is it true.
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> Message: 2
> Date: Wed, 18 Feb 2009 07:47:27 -0800
> From: Modeller Caretaker <>
> Subject: Re: [modeller_usage] Academic and Commercial
> To: salam pradeep <>
> Cc: 
> Message-ID: <>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> salam pradeep wrote:
> > Is there any variation in the models generated by the Academic 
> version> and the Commercial version of Modeller.
> > Some people say that the Modeller Academic version is not so 
> accurate in
> > generating the 3D models.
> > How far is it true.
> 
> That's not true at all. The commercial version differs from the 
> academiconly in two ways:
> 1. Academic Modeller treats MSE residues as equivalent to MET;
>   in commercial Modeller they are different residue types.
> 2. Commercial Modeller will not run without a valid license from
>   Accelrys. Academic Modeller needs a different license, from us.
> 
> Both versions should generate very similar models given the same 
> inputs.
> 	Ben Webb, Modeller Caretaker
> -- 
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 20 Feb 2009 15:39:50 +0100
> From: St?phane T?letch?a 	<>
> Subject: [modeller_usage] Using modeller with a web form: how topass
> 	the	provided key to modeller?
> To: 
> Message-ID: <>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> Hello,
> 
> I'm planning to provide models from carefully validated alignments 
> and 
> in order to provide this tool, i would like to allow users to 
> access to 
> the full model, and produce new ones using my methodology, from a 
> web 
> server.
> 
> According to the policy, http://salilab.org/modeller/FAQ.html#18, i 
> must 
> use a form and use this key for launching modeller (i totally agree 
> with 
> this).
> 
> However, how can i use this license?
> In fact, if i install modeller the standard way (on linux, using 
> http://salilab.org/modeller/9v6/release.html#rpm):
> env KEY_MODELLER9v6=XXXX rpm -Uvh modeller-9v6-1.i386.rpm, then the 
> key 
> is incorporated in the installation.
> 
> In this case, the "external" key is not used (mine is taken).
> 
> On the other end, if i install modeller without the key (remove the 
> env 
> KEY_MODELLER9v6=XXXX to the above command), i receive:
> 
> KEY_MODELLER9v5=<VALIDKEYHERE> /usr/bin/mod9v5 file.py
> Traceback (most recent call last):
>  File "<string>", line 1, in ?
>  File "/usr/lib/modeller9v5/modlib/modeller/__init__.py", line 65, 
> in ?
>    _modeller.mod_start()
> _modeller.ModellerError: check_lice_E> Invalid license key: xxx
> Go to http://salilab.org/modeller/ to get a license key,
> and then set the 'license' variable to it in the file
> /usr/lib/modeller9v5/modlib/modeller/config.py
> 
> 
> I have tried various combinations to set the KEY_MODELLER9v5 (env, 
> export, in a sourced file, etc) but i'm always stucked.
> 
> Any idea ?
> 
> Thanks a lot in advance,
> 
> St?phane T?letch?a
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