[gmx-users] Fwd: Restraints/constraints for keeping a helix as helical

[Mohsen Ramezanpour]

Dear All,

I was wondering if you have any comment or suggestion on this post.
Any comment is appreciated in advance.

Best,
Mohsen


---------- Forwarded message ----------
From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
Date: Wed, Aug 10, 2016 at 7:17 PM
Subject: Restraints/constraints for keeping a helix as helical
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Dear Gromacs users,

In my simulation, I am interested to keep specific part of an alpha-helix
(e.g. residues 10-15) as helical through whole production run. This has
been discussed a few time in mailing list but I could not get my answers.
Reading through Gromacs manual, and mailing list, I found three possible
ways as follows:

After making an index file (which has a group made of Backbone atoms of
residues 10-15, I will use genrestr to create:

1) a distance restraint file using option  -disre, and replacing the type'
from 1 to 2 manually.

OR

2) a constraint file using option  -constr, with type 2

as I leave other flags in genrestr as default values.

for distance restraints, I have replaced the type'= 1 with type'=2 based on
following quote from page 88 of manual-4.6.7 :

"...The type’ column will usually be 1, but can be set to 2 to obtain a
distance restraint that will never be time-and ensemble-averaged; this can
be useful for restraining hydrogen bonds."

I did this because a-helix can be helical if all the hydrogen bonds are
conserved during simulations.


3) The other and seemingly most appropriate way would be to apply "dihedral
restraints" of type 1 on Backbone atoms of residues 10-15.

As I understood, this can be done by making a [ dihedral_restraints ]
section in the topology file and providing correct angles and force
constants. However, unfortunately, I could not find any tools to generate
this .itp file automatically, like what is possible in making "distance
restraints" and "constraints".


Are you aware of any tool or script which generates the dihedral restraints
for an a-helix, capable of accepting an index file?

Which approach do you recommend for keeping an a-helix as helical?


Please let me know your opinion.

Thanks in advance
Cheers
Mohsen

-- 
*Rewards work better than punishment ...*



-- 
*Rewards work better than punishment ...*