[gmx-users] neutralizing membrane protein in lipid bilayer +water

[ram bio]

Dear Justin,

Thanks for the  suggestions and will be back after sometime after
following the trials.

Ram

On Tue, Sep 29, 2009 at 10:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> I was trying to model a part of the protein involved in the active
>> site and these terminal residues i think have no role in active site
>> as per the literature, so i was removing the residues whose
>> coordinates were not properly assigned (missing H atoms) so the
>> initial terminus changed to serine, we can even find such problems in
>> crystal structures where the coordinates don't get resolved
>
> Crystal structures never have H, but we simulate them all the time.  Their
> geometry is largely predictable :)
>
> Consider whether or not these deletions will have an effect.  While not
> catalytically active, do they have any role in maintaining the protein's
> structure?  Just my $0.02.  Don't chop out what doesn't seem to work; it
> might (or might not) be important.
>
> -Justin
>
>> properly...I think as the number of residues changed the total charge
>> also changed, these are some of the limitations that i think occur to
>> exactly predict the structure and activity for some proteins.
>>
>> Thanks
>>
>> Ram
>>
>> On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul <jalemkul at vt.edu>
>> wrote:
>>>
>>> ram bio wrote:
>>>>
>>>> Dear Justin,
>>>>
>>>>  Thanks and as per suggestion, now i have corrected the original
>>>> modelled pdb file and executed the pdb2gmx command with n-terminus
>>>> option 1 (NH2) and C-terminus option 1 (COOH), now the net charge is
>>>> 11.00, and the toplogy file has the first and last residues as under:
>>>>
>>>>
>>>>    1         NL      1    SER      N      1      -0.66    14.0067
>>>> ; qtot -0.66
>>>>    2          H      1    SER     H1      1       0.44      1.008
>>>> ; qtot -0.22
>>>>    3          H      1    SER     H2      1       0.44      1.008
>>>> ; qtot 0.22
>>>>    4        CH1      1    SER     CA      1      -0.22     13.019   ;
>>>> qtot 0
>>>>    5        CH2      1    SER     CB      2      0.266     14.027
>>>> ; qtot 0.266
>>>>    6         OA      1    SER     OG      2     -0.674    15.9994
>>>> ; qtot -0.408
>>>>    7          H      1    SER     HG      2      0.408      1.008   ;
>>>> qtot 0
>>>>    8          C      1    SER      C      3       0.45     12.011
>>>> ; qtot 0.45
>>>>    9          O      1    SER      O      3      -0.45    15.9994   ;
>>>> qtot 0
>>>>
>>>>  2950          N    285    PRO      N   1280          0    14.0067   ;
>>>> qtot 11
>>>>  2951        CH1    285    PRO     CA   1281          0     13.019   ;
>>>> qtot 11
>>>>  2952       CH2R    285    PRO     CB   1281          0     14.027   ;
>>>> qtot 11
>>>>  2953       CH2R    285    PRO     CG   1282          0     14.027   ;
>>>> qtot 11
>>>>  2954       CH2R    285    PRO     CD   1282          0     14.027   ;
>>>> qtot 11
>>>>  2955          C    285    PRO      C   1283       0.33     12.011
>>>> ; qtot 11.33
>>>>  2956          O    285    PRO     OT   1283      -0.45    15.9994
>>>> ; qtot 10.88
>>>>  2957         OA    285    PRO      O   1283     -0.288    15.9994
>>>> ; qtot 10.59
>>>>  2958          H    285    PRO     HO   1283      0.408      1.008   ;
>>>> qtot 11
>>>>
>>>> Please suggest if it is ok, so that i can continue with the further
>>>> steps.
>>>>
>>> No, that's your job as a scientist :)  Besides, I can't necessarily say.
>>>  Do
>>> those protonation states model reality?  Is your model a reasonable
>>> representation of a true physical system?  Does the net charge make
>>> sense?
>>>  Your original first residue was threonine, now it's serine.  What
>>> exactly
>>> was your "fix" to this problem?
>>>
>>> These are the things that you should always consider.  Only once you've
>>> solved these issues can you proceed with any degree of confidence.
>>>
>>> -Justin
>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> 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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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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