[EMAIL PROTECTED] wrote:
Dear colleagues,
I need to use simple distance restraints of 12.5 A between two CA atoms
of two residues. I am using the following lines in the .itp file
#ifdef DDISRES
[distance_restraints]
;ai aj type index type' low up1 up2 fac
1703 1712 1 0 1 11.5 12.0 12.5 1.0
The first feww line of .mdp file for minimisation of protein alone is
; Preprocessing
;
title = ${MOL}
cpp = /lib/cpp ;Preprocessor
define = -DDISRES ;For cg, and also steep
You are not actually applying your distance restraint. If you have "#ifdef
DDISRES," then you would have to "define = -DDDISRES" in the .mdp file. What
you probably meant to define was "#ifdef DISRES" in the topology.
After minimisation, the restarined residues & the adjacent
bonds break. This results in fragmnets - residues alone, peptide bond
alone and the rest of the protein. The distance restrained residues
seems to try to move towards each other (6.04 A after minimisation) and
this might have caused fragmentation. I tried to use various upper and
lower values for bond length so as to increase flexibility. But, still I
end up in the fragments.
Bonds don't break in classical MD, this is just an artifact of visualization,
probably from nasty steric clashes within your structure.
Some of the suggestions in the archive says VMD doesn't show
bonds if they r above threshold value. When I checked the distances
between the atoms, one of them is really long CO-CA bond 3.23 A
(normally its 1.59A). This means the bond is no longer there.
No, the bond is there, VMD just isn't smart enough to see it :) You are
probably well on your way to an explosion if you try to constrain bond lengths
with LINCS, however.
-Justin
I appreciate any suggestions in this regard.
Thanks & regards,
Latha.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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