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--- mutating_a_lipid [2024/02/20 16:50] – [Mutating a lipid] admin
+++ mutating_a_lipid [2024/02/20 16:53] (current) – admin
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 ======Mutating a lipid======
-Author: Eric Wang
+Authors: Eric Wang & Jeff Klauda
-Please email me at //ericzwang@gmail.com// if something isn't clear
+Please email me at //jbklauda@umd.edu// if something isn't clear
 Mutating a lipid means changing its chemical structure. We do this when our membrane contains a lipid which is not available by default in the CHARMM force field, but the structure is similar to an existing lipid. To mutate a lipid, you'll need to create your membrane with the pre-mutated lipids using CHARMM-GUI first.
-Once that is done, modify the relevant .str file to include your mutated lipid. See the following path on DT2 for an example for mutating CER240 to CER6. For small mutations, the IC table isn't necessary. \\
+Once that is done, modify the relevant .str file to include your mutated lipid. See the following path on ZT1 for an example for mutating CER240 to CER6. For small mutations, the IC table isn't necessary. \\
 ''/afs/shell.umd.edu/project/energybio/shared/jbklauda/scripts/mutate/toppar_all36_lipid_sphingo.str''
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 Then run **step5_input.inp** to create the namd input files. If you look in **step5_assembly.pdb**, your lipid should be renamed and its structure changed. Make sure there aren't any broken bonds.
-Finally, you will need to go into the namd subdirectory and validate that the restraints subdirectory has files with your new lipids listed. Moreover, you will need to make edits to the ''step5_input.colvar.str'' file to include reading in the new restraint (.ref) files in ./restraints and remove those that are no longer present in your model.
+Finally, you will need to go into the namd subdirectory and validate that the restraints subdirectory has files with your new lipids listed. Moreover, you will need to make edits to the ''step5_input.colvar.str'' file to include reading in the new restraint (.ref) files in ''./restraints'' subdirectory and remove those that are no longer present in your model.