I tried to run a MD simulation of a membrane protein. I have followed the Tutorial for Membrane Proteins (NAMD), using CHARMM36 force fields and a POPC lipid bilayer to embed my protein.
However I get this: FATAL ERROR: Unable to find dihedral parameters for CTL2 OSL PL OSL (17 23 20 24)
Where these atoms correspond to lipids.
I wonder if there is a problem in any of my parameters/topology files or a lipid-recognition problem when trying to construct the system
I would appreciate any advice or suggestion to solve this problem
Thanks in advance and best regards
That dihedral resides in the CHARMM toppar_all36_lipid_sphingo.str force field file. You need to specify that as one of your parameter files in the NAMD input.
Dear Dr. Lemkul
Thank you so much for your kind response. If I understood well, I should also include that force field file in my NAMD input. The problem is I haven't found it yet at: http://mackerell.umaryland.edu/charmm_ff.shtml Do you know where I could find it?
Thank you for your help
Hi Marlet, to prepare your system with the CHARMM force field just take a look at CHARMM-gui http://charmm-gui.org/
It is very usefull to prepare complex systems including membrane, etc ...
Dont hesitate to contact me for further help
Thank you so much both of you for your kinds responses.
Actually I have specified the file: toppar_all36_lipid_sphingo.str in my NAMD input file however i get this: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETERS LINE=*MASS 165 NHL 14.7000
I wonder how could I fix it, I guess I can not comment out this line. It is also weird because I am having problems since I am using force field parameters for CHARMM36 and not with CHARMM27.
Thanks in advance and best regards
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