[gmx-users] Average and bfactors.pdb

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin
Thank you so much for replyingAccording to the gromacs tuturial, i am trying to analyse my complex in terms of RMSD. In order to do that, first it is needed to obtain the average structure to get RMSD vs average structure . And average structure is a side product of obtaining RMSF. Is there anyway that i can calculate RMSD instead of geting RMSD vs average structure? If you want to caculate RMSD , wont you perform this way? 
Thanks in advanceFarial

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On Monday, August 21, 2017, 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:



On 8/20/17 11:48 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear justin
> Thank you for your replyIt means, there is no problem, i can ignore it ang go ahead?

Sure, but keep in mind that this "average structure" has no physical 
meaning.  The B-factors are (possibly) useful, but also keep in mind 
that solution dynamics and crystal dynamics are very different, so 
comparing the two may or may not be useful.

-Justin
> Sent from Yahoo Mail for iPhone
>
>
> On Monday, August 21, 2017, 2:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 8/20/17 11:51 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear gmx users
>> I removed jumps from my .xtc file before by using gmx trjconv and viewed my complex in vmd, it was ok and rhere was no jump. Now i use gmx rmsf and the same .xtc file which was created after using gmx trjconv, but when i view average. Pdb and bfactors.pdb files in pymol, my protein is still brocken. Would you please advice me how to solve this problem?
> There is no physical significance to an average set of coordinates.  These may
> appear broken or distorted.
>
> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>
> -Justin
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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