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

[Justin A. Lemkul]

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

-- 
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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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