Re: about angles in coordination complexes

From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Mon Jan 26 2015 - 11:51:11 CST

Dear Norman,
Dear Jerome,

I attempted using extrabonds as explained here (
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html), but the results
seems to be not affected.
No errors, no warnings.

Could you please have a look at the following data? they seems to me
reasonably formatted
*angle 1 20 5 1.35337 111.83119 # since atoms are based 0 I decreased of 1
the atom related entries*
*angle 1 20 7 0.768447 103.15240 # k is in Kcal/rad^2*
*angle 1 20 3 1.57934 122.83501 # ref in degrees*
*angle 3 20 5 0.939363 95.91890*
*angle 3 20 7 1.59095 98.25385*
*angle 5 20 7 0.832975 126.54048*

and I recall them using
*extraBonds on*
*extraBondsFile $parFolder/cobalt_extrabonds.txt*

I'll do meanwhile an attempt with the patches.

Thank you for your time,
Best,
Luca

2015-01-26 17:55 GMT+01:00 luca belmonte <lucabelmonte_at_gmail.com>:

> I am already familiar with patches and I have to admit that I never
> thought to them under this perspective.
>
> I'll try with the solution proposed by Norman and with the patch.
>
> Thank you for the suggestions.
>
>
>
> 2015-01-26 17:50 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>
>> You'll need to create and apply a patch, which is like a special residue
>> that modifies an existing topology.
>> http://www.charmm.org/documentation/c34b1/struct.html#%20Patch
>>
>> You can find an example in the standard CHARMM topology for proteins is
>> you look for the patch for disulfide bonds (called DISU).
>>
>> That patch is applied in the following psfgen example:
>> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node17.html
>>
>> Jerome
>>
>>
>> On 26 January 2015 at 17:28, luca belmonte <lucabelmonte_at_gmail.com>
>> wrote:
>>
>>> Yes, in the QM calculations I have all of them, but I did not mapped
>>> them into the par file.
>>>
>>> What I have done is to map everything related to the methanethiol group
>>> of the cysteine residue of the top/par files but I did not mapped any angle
>>> between the sulphurs of different cysteines (the S-M2+-S angle you said).
>>>
>>> Could you please provide me any example, keyword or manual reference to
>>> do that?
>>>
>>>
>>> 2015-01-26 17:20 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>
>>>> What I said was very generic. Now looking at the specific arrangement,
>>>> it should be possible to reliably enforce a tetrahedral shape with 6 S-Mg-S
>>>> angle potentials. Do you have those in your model? If yes maybe there's a
>>>> problem with them.
>>>>
>>>> Jerome
>>>>
>>>> On 26 January 2015 at 17:02, luca belmonte <lucabelmonte_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Jerome,
>>>>>
>>>>> Thank you for the reply.
>>>>>
>>>>> At the very beginning of the story I was wondering to do as you
>>>>> suggest.
>>>>> But then I encountered some difficulties. Probably I lack the correct
>>>>> keyword to map the dihedral angle between different residues.
>>>>>
>>>>> Do you have some hint?
>>>>>
>>>>> Thank you,
>>>>> Luca
>>>>>
>>>>> 2015-01-26 16:56 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>>
>>>>>> Hi Luca,
>>>>>>
>>>>>> > These complexes were previously parameterized with GAMESS US,
>>>>>> results of its jobs mapped (to the top and par files)
>>>>>>
>>>>>> You didn't say what exactly they were mapped to, but your results
>>>>>> indicate that the empirical description you have now is not sufficient to
>>>>>> describe the geometric constraints around your metal center.
>>>>>>
>>>>>> You probably need more angle/dihedral/improper dihedral terms. I
>>>>>> would include them in the top/par files rather than extraBonds, because
>>>>>> they will be an essential part of your custom force field.
>>>>>>
>>>>>> Jerome
>>>>>>
>>>>>>
>>>>>> On 26 January 2015 at 16:28, luca belmonte <lucabelmonte_at_gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Thank you for the hint!
>>>>>>>
>>>>>>> Best,
>>>>>>> Luca
>>>>>>>
>>>>>>> 2015-01-26 16:24 GMT+01:00 Norman Geist <
>>>>>>> norman.geist_at_uni-greifswald.de>:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I think you are less interested in fixing or positional harmonic
>>>>>>>> restraints, rather than in defining additional bonds/angles/dihedral to
>>>>>>>> maintain your conformation. this can be done quite easy using the
>>>>>>>> "ExtraBonds" interface of NAMD. Please find details in the manual.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Norman Geist.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>>>>>>> Auftrag von *luca belmonte
>>>>>>>> *Gesendet:* Montag, 26. Januar 2015 15:39
>>>>>>>> *An:* namd-l_at_ks.uiuc.edu
>>>>>>>> *Betreff:* namd-l: about angles in coordination complexes
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Dear Namd users,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I am pretty new to this mail list, so... nice to meet you.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Let me introduce briefly the target. I want to simulate several
>>>>>>>> small complexes made of small peptides. In these peptides cysteines always
>>>>>>>> coordinate a transition metal dication (M2+). The purpose is to have a
>>>>>>>> guess of the stability of the complexes by mean of internal energy
>>>>>>>> estimation.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> The complexes are "rubredoxin" likes, and you can look at
>>>>>>>> coordination sphere as follows:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Cys Cys
>>>>>>>>
>>>>>>>> \ /
>>>>>>>>
>>>>>>>> M2+
>>>>>>>>
>>>>>>>> / \
>>>>>>>>
>>>>>>>> Cys Cys
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> All the complexes on which I am working on have tetrahedral
>>>>>>>> coordination shapes, in which the M2+ is in the middle of the cage, while
>>>>>>>> cysteines sulphurs are at vertexes.
>>>>>>>>
>>>>>>>> These complexes were previously parameterized with GAMESS US,
>>>>>>>> results of its jobs mapped (to the top and par files) and till know
>>>>>>>> everything is fine.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Now comes the problem. When I look at the shape of the coordination
>>>>>>>> complex, after the minimization, I expect to see a tetrahedral
>>>>>>>> coordination, but the result is a non common shape in which the M2+ pop out
>>>>>>>> from the coordination plane.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> To address this issue I was wondering to fix the sulphur atoms
>>>>>>>> positions around the cluster using fixedAtoms, but I am scared that this
>>>>>>>> approach can affect calculations, providing wrong energy values. Do you
>>>>>>>> think so? Do you have another strategy to overcome this problem?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Any hint is welcome,
>>>>>>>>
>>>>>>>> Thank you in advance,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> Luca Belmonte, PhD
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Luca Belmonte, PhD
>>>>>>>
>>>>>>> CIBIO - Center for Integrative Biology
>>>>>>> University of Trento
>>>>>>>
>>>>>>> Phone: +39 0461 28 53 41
>>>>>>> Mobile: +39 328 45 81 762
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Luca Belmonte, PhD
>>>>>
>>>>> CIBIO - Center for Integrative Biology
>>>>> University of Trento
>>>>>
>>>>> Phone: +39 0461 28 53 41
>>>>> Mobile: +39 328 45 81 762
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Luca Belmonte, PhD
>>>
>>> CIBIO - Center for Integrative Biology
>>> University of Trento
>>>
>>> Phone: +39 0461 28 53 41
>>> Mobile: +39 328 45 81 762
>>>
>>
>>
>
>
> --
> Luca Belmonte, PhD
>
> CIBIO - Center for Integrative Biology
> University of Trento
>
> Phone: +39 0461 28 53 41
> Mobile: +39 328 45 81 762
>

-- 
Luca Belmonte, PhD
CIBIO - Center for Integrative Biology
University of Trento
Phone: +39 0461 28 53 41
Mobile: +39 328 45 81 762

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