Hello all
I am study water mediated protein-DNA interaction.
What I have did remove all crystalized water and add TIP3P water 6 angatrsom
from protein-DNA surface.
Minimize first water + ions then finally whole system
Heat the system from 0 to 300K at NVT for 200ps using positional restraint on
protein-DNA
Decrease positional restraint for 200ps at NVT
Equilibrate the system at NPT for 600ps
Production MD for 6ns
I have generated prmtop for system have 10 water molecules
When I visualize trajectory using above prmtop water moleclues are so far from
mask residue
Though when I check number of water moleclues around mask residue using
watershell command lower range 3 angostrom
and upper range 5 angostrom, water molecules are present at both range.
I am not getting why processed trajectry not showing water molecule close to
mask residue.
With regards
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sun Apr 03 2011 - 09:00:03 PDT
