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

[ram bio]

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
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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>