I have to simulate DPPC+Water. For that I am using a surfactant SDS. I have downloaded .itp file of surfactants. But I need a gro file(coordinate file). How I get that file for SDS?
convert your SDS.pdb file to .gro file using open babel or try PRODRG server to get .itp and .gro file of your SDS
Visit to following web site and download SDS.pdb file and convert it in your format
http://xray.bmc.uu.se/hicup/SDS/
Hello Sagar,
Thanks for your Suggestion. My problem has been solved .Actually my problem is that in
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters/57-surfactants
from this link I have downloaded .itp file. For SDS there are four beads. SO3,C1,C2,C3. So I can not generate any gro file. Which is for this topology.
But on the martini site there is a special tool , which can create gro file from itp.
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