Dear Amber users:
I would like to use a pre-equilibrated system formed by a DPPC lipid membrane plus a protein to run MD with Amber. My problem comes up when I try to convert the lipids to Lipid 14 PDB format in order to obtain the topology and coordinate files in Leap. The atom nomenclature in the conversion table charmmlipid2amber.csv is almost completely different to that on my pdb (the scriptcharmmlipid2amber.py it is thought to be used with a membrane built with Charmm GUI). One the other hand, I have tried to convert my file with the tool pdb reader of the website Charmm GUI with no results.
Before writing a script changing the nomenclature of my file, I would like to know If someone has had this problem before or if such a script already exits.
Thanks a lot
Cheers
Raquel Romero
Department of Pharmaceutical and Biological Chemistry
UCL School of Pharmacy, University College London
29/39 Brunswick Square
London
WC1N 1AX
T: 0207 753 5972
E: raquel.romero.12.ucl.ac.uk
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Received on Mon Dec 08 2014 - 11:00:02 PST
