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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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DPPC alkyl chain length #8

Closed Navya321 closed 6 years ago

Navya321 commented 6 years ago

Problem is with respect to the force field parameters of the lipid bilayer: dppc (Dipalmitoylphosphatidylcholine) molecule.

Issue Information

Software name & Version : web service LigParGen

Expected Behavior

Force field parameters should be available

Actual Behavior

The opls-aa force field parameters are available when I keep the chain length of the dppc (Dipalmitoylphosphatidylcholine) molecule to 7 Carbon atoms, however, when I increase it to 14 the service shows error. It pointed me to post the error on this forum. It would be great if the authors would fix this error. Also, I feel that the parameters for the alkyl chain CH2 groups won't really change so it shouldn't be a problem if I put 10 Carbon atoms or hundred. Number of atoms in my molecule is 130 (less than the limit value of 200).

Regards, Navya IIT Guwahati India

leelasd commented 6 years ago

This server is not designed for Lipid molecules. You should look at recent publications on OPLS-AA Lipid force fields for that. @Navya321 also please attach pdb/mol file, whatever input you used, to exactly diagnose what the problem is.

Navya321 commented 6 years ago

Thanks for the quick response.

Sure, I will sift through the recent publications for the same. I was using the Draw Molecule feature, so there is no pdb/mol file; the molecule was DPPC.

Further, it would be great if you all can come up with an added tool for lipid force field parameters.

Great work though. Cheers.

leelasd commented 6 years ago

@Navya321 Sorry Cannot really help if I don't have an input. Lipid molecules are extremely sensitive to parameterization and need to be carefully crafted, and is beyond the scope of the server.
Best wishes, Leela