On 3/15/13 8:50 AM, Shima Arasteh wrote:
Dear users,
Although I put the position restraints on backbone, I get RMSD around 0.2 nm.
Is it usual?
No, 0.2 nm is very high. With position restraints, offhand I would think around
0.05 nm or less would be indicative of proper restraints.
This deviation is just for a minimization step only. I' m on doubt about
keeping the backbone in a fix secondary structure.
I' d prefer to restraint the backbone completely. Is it possible?
Yes, using genrestr to create a suitable posre.itp file that includes only
backbone atoms.
-Justin
Thanks in advance.
Restraints allow, by definition, for slight deviations.
Erik
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Dear gmx users,
I want to use restraints on backbone of my protein to keep its secondary
structure during minimization and equilibration steps. To do so, I
generated backbone-restrain.itp and then included it to top file. Next,
added define = -DPOSRES to minim.mdp file.
After minimization, when I check the minimization output file, I saw
that the backbone of input and output files are not exactly the same.
Is there any step which I have not done to set the restraints correctly?
Thanks in advance.
Sincerely,
Shima
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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