[gmx-users] define a new residue

Sun Jul 8 17:29:16 CEST 2012

Thanks all.
So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right?

Sincerely,
Shima

________________________________
From: francesco oteri <francesco.oteri at gmail.com>
To: jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Cc: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Sent: Sunday, July 8, 2012 4:44 PM
Subject: Re: [gmx-users] define a new residue

Usually in CHARMM the sidechains are parametrized as separate blocks and than merged to the backbone.
In fact backbone, in charmm aminoacids, have always tha same charges. 

So if the same strategy has been used for you residue (you should read the paper reporting the parameterization),
you can simply use the standard backbone charges.
If this is not the case, You have to develop you charge set.

2012/7/8 Justin A. Lemkul <jalemkul at vt.edu>

>
>On 7/8/12 7:10 AM, Shima Arasteh wrote:
>
>Because I saw that residues defined in aminoacids.rtp file don't have H in their carboxyl and atom N. So I decided to remove H !
>>
>>
>
Chemically, there is never an H atom on the C-terminal carbonyl of a group involved in a peptide bond.  If you parameterized a molecule that was protonated in such a way, it will give an erroneous output.  You can't just delete atoms, and shifting the charge by adding it back somewhere else is also very suspect, because you're changing the electronic nature of the compound.
>
>I would say you need a better parameterization protocol using a more suitable model compound.
>
>-Justin
>
>
>
>
>>
>>
>>Sincerely,
>>Shima
>>
>>
>>________________________________
>>From: francesco oteri <francesco.oteri at gmail.com>
>>To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>>Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Sent: Sunday, July 8, 2012 3:28 PM
>>Subject: Re: [gmx-users] define a new residue
>>
>>
>>Why have you removed the hydrogen?
>>
>>
>>2012/7/8 Shima Arasteh <shima_arasteh2001 at yahoo.com>
>>
>>Dear Francesco,
>>
>>Thanks. Honestly I thought about this, but I don't know how much charges I need to increase or decrease of other atoms?
>>>
>>>Is it possible to add the FVAL with the H atom( which I removed before)? I mean that I apply the complete formyl-valine and don't remove the H atom.
>>>
>>>Thanks for your suggestions.
>>>
>>>
>>>Cheers,
>>>Shima
>>>
>>>
>>>
>>>________________________________
>>>From: francesco oteri <francesco.oteri at gmail.com>
>>>To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>Sent: Sunday, July 8, 2012 3:04 PM
>>>Subject: Re: [gmx-users] define a new residue
>>>
>>>
>>>
>>>Hi Shima,
>>>usually charge calculation are carried out on the system that is supposed to be used in the MD.
>>>So in my opinion you shouldn't remove the hydrogen.
>>>Anyway, if you wanna remove the hydrogen, either you increase the charge of some other atom or
>>>calculate the charges on the new residue without hydrogen.
>>>
>>>Francesco
>>>
>>>
>>>2012/7/8 Shima Arasteh <shima_arasteh2001 at yahoo.com>
>>>
>>>Hi dear gmx friends,
>>>
>>>
>>>>I got the parameters of formyl-valine through the CHARMM website. Now I need to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file. To set the correct charges for atoms, I used the CHARMM output. In order to define FVAL to rtp file, I added these lines as below:
>>>>
>>>>CN    C    0.349    0
>>>>     ON    O    -0.494    1
>>>>     H1    HC    0.100    2
>>>>     N    NH1    -0.423    3
>>>>     HN    H    0.09    4
>>>>     CA    CT1    0.144    5
>>>>     HA    HB    0.09    6
>>>>     CB    CT1    -0.097    7
>>>>     HB    HA    0.09    8
>>>>     CG1    CT3    -0.268    9
>>>>     HG11    HA    0.09    10
>>>>     HG12    HA    0.09    11
>>>>     HG13    HA    0.09    12
>>>>     CG2    CT3    -0.268    13
>>>>     HG21    HA    0.09    14
>>>>     HG22    HA    0.09    15
>>>>     HG23    HA    0.09    16
>>>>     C    C    0.209    17
>>>>     O    O    -0.395    18
>>>>
>>>>As you see I omitted the H connected to Carboxyl. Now the total charge of the new-defined residue is not zero (-0.333) . How can I correct it?
>>>>
>>>>
>>>>I would appreciate you for your suggestions.
>>>>Thanks in advance.
>>>>
>>>>Sincerely,
>>>>Shima
>>>>--
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>>>>
>>>
>>>--
>>>Cordiali saluti, Dr.Oteri Francesco
>>>
>>>
>>
>>
>-- 
>
========================================
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>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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-- 
Cordiali saluti, Dr.Oteri Francesco