I want to build the topology file of lipid and water. How to create the topology file of the attached dmpc.gro molecule by Gromacs? I don't want to download the dmpc_topol.top from Tieleman sites.
Please help if you've done this before.
Thanking You
Bikash
Osaka, Japan
If you use the GROMOS ff, and you do not want to use Tieleman topology (I do not understand why, because you need to validate your new topology)...you need to create your own residue on the gromos ff: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=ff
If not, you can choose to use the charmm 27 ff, where you have a topology for DMPC, and it is not the Tieleman's one. But you need to edit your file, and name the residue DMP to DMPC. Then you put in your terminal:
pdb2gmx -f dmpc.gro -o out.gro -p topol.top
and you choose charmm27.ff
If you do not want to use the Tieleman's site, but you agree to use the Gromacs site, you can download the LipidsForGro96_53a6.zip , from: http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
And there you have the validate topologies for many lipid molecules, too.
Regards
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