On 10/31/19 6:02 AM, shakuntala dhurua wrote:
thank you sir, by this gmx trjconv -center -pbc mol the two chains are
coming closer but still rmsd result is high and fluctuating highly while
taking two chain at a time. please suggest me to calculate resonable rmsd
value for full protein
If you have very flexible regions, the RMSD value will be high. That's
not necessarily wrong. If you've corrected the imaging issue that led to
spurious increases in RMSD, this is the actual value. Whether or not it
makes sense to consider the dimer as a whole in RMSD is another issue,
but it depends on what you want to calculate and you need to be
judicious in your selections for fitting and calculation groups,
especially in the case of flexible termini or disordered regions.
-Justin
On Wed, Oct 30, 2019 at 7:52 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 10/30/19 9:39 AM, shakuntala dhurua wrote:
i have generated trr file for a protein containing two chains .during the
simulation two chains are going at two different sides of the box. so the
RMSD results are abruptly high (near 35-40 angstrom). To create a image
of
one chain at the same side of other chain,i used the following command by
removing pbc
==============
try1. trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur compact
try2.trjconv -s tpr -f .trr -o .xtc -pbc nojump
try3. -f a.mdp -c a_cluster.gro -o a_cluster.tpr
try4 trjconv -s a.tpr -f .trr -o xtc -fit rot+trans
==============================
still similar results are coming. but for each chain,RMSD value is
reasonable.
kindly suggest some way to calculate RMSD value for full protein
Create an index group for one protein and use it to center the
coordinates. This will re-wrap the whole complex into the central image.
gmx trjconv -center -pbc mol
-Justin
On Wed, Oct 30, 2019 at 4:59 PM rajat punia <rjtpu...@gmail.com> wrote:
make sure you superimpose the structures using -fit flag.
On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua <
madhu.dhuru...@gmail.com>
wrote:
actually I am using insulin protein system, i have calculated rmsd but
that
is too high which is approx 40 amstrong which is not supposed to be ,
and
initially during energy minimization two chain go far away from each
other.
I have used flag like trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur
compact
trjconv -s .tpr -f .trr -o .xtc -pbc nojump etc but still result is
same
.
so please suggest me to solve this problem.
--
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
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
*Regards,*
*Rajat Punia*
*PhD Chemical Engineering*
*IIT Delhi*
*+91-9821210386*
--
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
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
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
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
