On 10/12/12 2:42 AM, tarak karmakar wrote:
Dear ALL,
In my protein I need to constraint the length between the Metal and
the N of Histidine residues. In the .rtp file I didn't specify this
Mn-N connectivity; these are more or less coordinate bonds. So to do
that I specified the Mn, N-atom indices and the corresponding lengths
in the topology file, part of it is given below
[ constraints ]
; index1 index2 funct length(nm)
6062 6063 1 0.11490000000
6062 6064 1 0.11490000000
6060 4309 1 0.21000000000
6060 4268 1 0.22700000000
6060 4979 1 0.22600000000
In the .mdp file I have included the following lines
constraints = h-bonds ; covalent h-bonds constraints
constraint_algorithm = LINCS ; LINear Constraint Solver
continuation = yes ; apply constraints to the
start configuration
lincs_order = 4 ; highest order in the
expansion of the contraint coupling matrix
lincs_iter = 1 ; number of iterations to
correct for rotational lengthening
lincs_warnangle = 30 ; [degrees] maximum angle that
a bond can rotate before LINCS will complain
[ I followed the above mentioned protocol and I see Mn-N distances are
not changing during the simulation, so served my purpose.]
So for all sorts of specified constraints (H-covalent bonds, Mn-N
coordinate bonds), MD will make use of LINCS algorithm !! . But my
query is about whether LINCS will be equally applicable as that of for
covalent bonds in constraining Mn-N distances where the real(?)
bonds(connectivity) don't exist !!
Differentiating bond types ( covalent or coordinate) by means of
connectivity information.
There is no such differentiation, at least in normal molecular mechanics force
fields. You're telling mdrun that there are constraints in the system, and it's
applying them. It has no intuition as to the chemical nature of these
bonds/constraints. You can constrain any distance you like in a system via
LINCS or SHAKE (chosen in the .mdp file, LINCS is default).
-Justin
--
========================================
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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