On 7/15/16 4:56 AM, roshanak starlight wrote:
excuse me i forgot that write subject.
On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <starlight....@gmail.com
wrote:
hello
i use kalp-15 in dppc tutorial that there is in this website :
http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
-fc 100000 100000 100000 which shoud i choose ? ( i choose 1:protein .
is it right ?)
From the tutorial:
"The authors of the InflateGRO script recommend using a very strong
position-restraining force on protein heavy atoms to ensure that the position of
the protein does not change during EM."
So choose the protein heavy atoms (Protein-H).
2.where should i add a line "define = -DSTRONG_POSRES" in minim.mdp ? i
add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
thank you
It doesn't matter.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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