[gmx-users] Re: change in secondary structure

[bharat gupta]

Thanks for ur kind reply Justin ...

I also searched the gmx userlist regarding the same query and I found out
that It was mentioned to repeat the simulation again with a different force
field .. but I don't know about the energy minimization parameters as  I am
following ur lysozyme tutorial  for that .. I will get back to u get if I
get the same type of structural changes with this force field...

Also I would like to mention one more thing .. as I did the simulation of
crystal str of GFP with the same parameters which I used for the variant of
GFP .. In case of the crystal str. simulation result, it seems to be
perfectly fine and there is no change in the secondary structure also ...
So, if I am not wrong then there is some problem with the variant structure
that I have modeled ??.. Actually the variant of GFP that I have modeled has
one loop (of 4 amino acid in original str) replaced with an another loop of
9 residues length ... CAn this be the reason ??

Regarding the simulation time I want to ask ... what is the minimum or the
optimal time the structure should be simulated for such analysis as I have
read many paper published in big journals doing simulation only for 1ns (in
that case I am doing for 3 ns)... pls comment

On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> Hi,
>>
>> I think I have asked this question earlier in the forum .. that during my
>> 3ns simulation of a 230 amino acid proteins some portion of 2 beta strands
>> got converted to loop/random coil, after visualizing in VMD. I checked the
>> DSSP profile also .. and as per the DSSP results it's coil in that region ..
>> can anybody tell me where can the error be as I have been checking my
>> structure right from the minimization step till npt equilibration and its
>> was fine ... this has happened only after simulation ... pls help ??
>>
>
> The comments I made last week still stand:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html
>
> You're basing your conclusions on a 3-ns simulation, which I would say is
> far too short to obtain any meaningful data for such a system.
>
> -Justin
>
>  --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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