Hi AMBER users,
I tried to embed a protein in a POPC lipid bilayer using VMD. The generated pdb is unrecognised by amber. It has weird atom names that are not present in the lipid forcefield file or its extension.
A sample is here:
ATOM 1 N POPCL 1 -33.304 -39.250 20.920 1.00 0.00 L11 N
ATOM 2 C12 POPCL 1 -32.577 -38.468 22.038 1.00 0.00 L11 C
ATOM 3 H12A POPCL 1 -31.812 -37.824 21.442 1.00 0.00 L11 H
ATOM 4 H12B POPCL 1 -32.055 -39.156 22.715 1.00 0.00 L11 H
ATOM 5 C13 POPCL 1 -33.428 -38.491 19.695 1.00 0.00 L11 C
ATOM 6 H13A POPCL 1 -32.514 -37.985 19.477 1.00 0.00 L11 H
same for the water and ions.
Is there a trick to convert the file to an AMBER-friendly format?
Regards,
Mohammad
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Received on Sat Apr 28 2018 - 15:30:02 PDT
