#ZHAO LINA# wrote:
Thanks for your answer.
How can I tell which ones I should restrain? all no-H atoms? in most general
situations.
For the sake of clarity in the archive, it's probably best to avoid broad
generalizations. People can easily stumble upon a post and take it way out of
context. A "general situation" might encompass a lot. I will reiterate that if
you want to recapitulate the behavior of pdb2gmx with respect to typical
biomolecules, you should choose all non-H atoms.
If you have some other specialized application, I can make no recommendation,
nor can anyone else, in the absence of a more thorough description.
-Justin
lina
________________________________________
From: [email protected] [[email protected]] on behalf
of Justin A. Lemkul [[email protected]]
Sent: Wednesday, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
Hi,
When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.
A little naive questions, but I do do not know.
The answer depends on your needs. When running genrestr without an index file,
you can choose from any of the default groups. If you provide an index file,
any group can be chosen.
The default behavior of pdb2gmx is to generate a posre.itp file that restrains
all heavy (non-H) atoms. You can do the same with genrestr if you want, but
again, the atoms you want to restrain depend on your goals.
-Justin
Thanks with regards,
lina
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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