[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Thu Nov 10 09:36:32 CET 2011 

Thanks Mark,

1) By the way do you know any database where I could obtain information
about function of the specific CAP groups ?
E.g as I know the most spread CAP on N is ACE group but in my case there is
For ( simple COH group) instead of ACE.

I think that parametrisation of such simple groups should not be very
complicate but it's strange that I've not found already built topology for
them.


2) Also I've tried to made topology for D amoniacids. I've started with the
topology of L analogs e.g for D-val I've created enty based on the Val in
.rtp and .hdb files. Not I think I should to invert impropers for the
Calpha atoms that new topology represent to true D-isomer :) But I'm not
sure about how to make it correctly :)

In .itp I've found for new DVA residue

 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
   CA     N     C    CB     gi_2
   CA   CG1   CG2    CB     gi_2
    C    CA    +N     O     gi_1

here there are 2 enties for the Ca atoms. What should I do with it for
invertion?

James


2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au>

>  On 10/11/2011 7:05 PM, James Starlight wrote:
>
> Justin,
>
>
> I've also look for the cap editing in the pymol but it seems that that
> function lacks in that program
>
> By the way, what are specificity of such Cap groups ? Do they are only
> sheld charges on the termi or have something addition function?
>
>
> They can. The purpose of a simulation is to provide a model of reality.
> How one would wish to cap a peptide depends what is being modelled under
> what conditions with what objectives in mind.
>
>
>
> What difference beetwen different caps I cant understand why in my
> structure there are so non-standart groups.
>
>
> Shrug. We don't even know what they are... Wherever you sourced your
> starting structure should discuss how and why the termini have such caps.
>
> Mark
>
>
>
>
> James
>
> 2011/11/9 Justin A. Lemkul <jalemkul at vt.edu>
>
>>
>>
>> James Starlight wrote:
>>
>>> Justin,
>>>
>>> Could you tell me another alternative ways to replace existing cap
>>> groups in my pdb besides xleap ? ( I've had  many problems with the pdb's
>>> processed by this soft). Also I've tried to make topology for the
>>> non-standart caps by PRODRG but I also have some problems with such
>>> parametrisation.
>>>
>>>
>>  Unless you describe your problems, there's very little anyone can or
>> will try to do to help you.  I've never had a problem with an xleap
>> coordinate file, so I can't offer you any additional guidance with that.
>>  Otherwise, there are dozens of programs that are capable of drawing
>> molecules or editing files.  See, for instance:
>>
>> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>>
>> -Justin
>>
>>
>>> Also I've not found suitable topology for some D-isomers ( it's strange
>>> that parametriation for such typical non-standart residues is absent in all
>>> force fields ). As I understood I cant use topology of L-analogs for the
>>> parametrisation of such D-forms because I dont know suitable parameters for
>>> dihedrals for instance.
>>> Have someone pre-built parameters for the D-aa for Gromos or Charmm
>>> force field?
>>>
>>>
>>> Thanks,
>>>
>>> James
>>>
>>>  2011/10/29 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>>
>>>
>>>
>>>
>>>    James Starlight wrote:
>>>
>>>        Justin, hello!
>>>
>>>        Could you tell me what exactly program from the Amber tools
>>>        package you've used for the KALP peptide preparation e.g for
>>>        capping ?
>>>
>>>
>>>    xleap
>>>
>>>    At this point, please start a new thread for your questions, as
>>>    these topics are completely unrelated to where you started.
>>>
>>>    -Justin
>>>
>>>
>>>     --     ==============================__==========
>>>
>>>
>>>    Justin A. Lemkul
>>>    Ph.D. Candidate
>>>    ICTAS Doctoral Scholar
>>>    MILES-IGERT Trainee
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
>>>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>>>    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>>    ==============================__==========
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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