Dear community,
I am running simulation of a protein which
contains water molecules in its pdb file. I have prepared topology and
coordinate files by retaining the water molecules present in the pdb file.
By regenerating the pdb file with the help of ambpdb the protein atom and
water molecule oxygen atom numbers and distance in which I am interested are
1735, 2946 and 1.85717666 A respectively. So I prepared the following file
to keep the distance between this two atoms constant
filename: rst.dst
#
# Change in distance
&rst
ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 1.85717666, r2= 1.85717666, r3=
1.85717666, r4= 1.85717666,
rk2=0.0, rk3=320.0, ir6=1, ialtd=0,
&end
My input file for minimization of only the water molecules is as bellow
filename: min.in
minimisation with solute restrain
&cntrl
imin=1,maxcyc=500,ncyc=250
ntpr=5,ntr=1, nmropt=1,
restraint_wt=1000.0
restraintmask=':1-164', #my protein contains 164 residues
/
&wt type='END' /
DISANG=rst.dist
But after minimization is over the atoms of interest (numer: 1735 and 2946)
are not remaining in the same distance. I am not able to understand where I
am going wrong. Please help. Thank you in advance.
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Mon Apr 18 2011 - 03:00:03 PDT
