[gmx-users] Average and bfactors.pdb
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?
Best Farial
Sent from Yahoo Mail for iPhone
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Re: [gmx-users] Average and bfactors.pdb
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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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Re: [gmx-users] Average and bfactors.pdb
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?
Sent from Yahoo Mail for iPhone
On Monday, August 21, 2017, 2:34 AM, Justin Lemkul 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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
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Re: [gmx-users] Average and bfactors.pdb
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 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
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
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Re: [gmx-users] Average and bfactors.pdb
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
Sent from Yahoo Mail for iPhone
On Monday, August 21, 2017, 5:24 PM, Justin Lemkul 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 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
>
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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Gromacs Users mailing list
* Please search the archive at
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Re: [gmx-users] Average and bfactors.pdb
On 8/21/17 5:25 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; } 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?
I normally compute RMSD vs. the equilibrated structure or vs. the
crystal structure, not an average structure.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Average and bfactors.pdb
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear justin
Thanks alot for your advice
Sent from Yahoo Mail for iPhone
On Thursday, August 24, 2017, 5:51 AM, Justin Lemkul wrote:
On 8/21/17 5:25 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; } 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?
I normally compute RMSD vs. the equilibrated structure or vs. the
crystal structure, not an average structure.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe requests visit
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