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

[Justin A. Lemkul]

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
>>
>> ========================================
>> _______________________________________________
>> 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
>>
> 

-- 
========================================

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

========================================