[gmx-users] EM problem for homology model !!

[narender]

Dear Users,
Hi, i am getting problems in doing energy minimizing of my system of 3400 
atoms (371 residues). This system is a homology build protein and i want to 
do atleast 1000 steps of steepest descent. But its converginh to Fmax after 
just 4 steps . I tried changing emtol and emstep but of no use.  
Please help !!. Also it would be great if someone could tell me how can i fix 
my protein's backbone and minimize only the sidechains.

thank in advance
NSM


 (My EM input file (.mdp is) 

;
cpp                 =  /lib/cpp
define              =  -DPOSRE
constraints         =  all-bonds
integrator          =  steep
nsteps              =  1000
;
;       Energy minimizing stuff
;
emtol               =  2300
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
~
~
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