toppar files are from the toppar_c36_jul20 directory available on http://mackerell.umaryland.edu/charmm_ff.shtml
toppar files have been modified to be used with Charmm and Namd
 

par_all36m_prot.prm									
par_all36_na.prm									
par_all36_carb.prm									
par_all36_lipid.prm									
par_all36_cgenff.prm							

top_all36_prot.rtf										
top_all36_na.rtf									
top_all36_carb.rtf										
top_all36_lipid.rtf											
top_all36_lipid_header.rtf					-> top_all36_lipid.str without lipid topologies			
top_all36_cgenff.rtf						-> CHOL residue is renamed CHOLI			

toppar_water_ions.str 						-> Charmm commands have been commented			
toppar_dum_noble_gases.str					-> Charmm commands have been commented	 		
toppar_ions_won.str							-> Charmm commands have been commented	 			

toppar_all36_prot_arg0.str 	 	
toppar_all36_prot_c36m_d_aminoacids.str 	-> Charmm commands have been commented			
toppar_all36_prot_fluoro_alkanes.str 				
toppar_all36_prot_heme.str							
toppar_all36_prot_na_combined.str					
toppar_all36_prot_retinol.str						
toppar_all36_prot_modify_res.str					

toppar_all36_lipid_bacterial_para.str 		-> toppar_all36_lipid_bacterial.str without lipid topologies and with Charmm commands commented			
toppar_all36_lipid_bacterial.str 	 
toppar_all36_lipid_cardiolipin.str 	 
toppar_all36_lipid_cholesterol_para.str 	-> toppar_all36_lipid_cholesterol.str without lipid topologies and with Charmm commands commented			
toppar_all36_lipid_cholesterol.str 	 
toppar_all36_lipid_inositol.str 	 
toppar_all36_lipid_lps_para.str 			-> toppar_all36_lipid_lps.str without lipid topologies			
toppar_all36_lipid_lps.str 	 
toppar_all36_lipid_miscellaneous_para.str 	-> toppar_all36_lipid_miscellaneous.str without lipid topologies			
toppar_all36_lipid_miscellaneous.str 	 
toppar_all36_lipid_model.str 	 
toppar_all36_lipid_prot_para.str 			-> toppar_all36_lipid_prot.str without lipid topologies				
toppar_all36_lipid_prot.str 	 
toppar_all36_lipid_sphingo_header.str 		-> toppar_all36_lipid_sphingo.str without lipid topologies and with Charmm commands commented				
toppar_all36_lipid_sphingo_para.str 		-> toppar_all36_lipid_sphingo.str without lipid topologies and with Charmm commands commented			
											-> the following lines have been added from toppar_all36_lipid_sphingo-website.str available at http://terpconnect.umd.edu/~jbklauda/ff.html
	!Edited by Dr. Klauda and Eric 3/17
	CTO1 CTO1  222.500     1.500   ! alkanes, 3/92: CTL1 CTL1
	CTO1 CTL2  222.500     1.538   ! alkanes, 3/92: CTL1 CTL2
	CTO1 C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO: CT1-C
	! following changes made by Dr. Klauda and Eric 3/17
	CTL1   CTO1   CTO1    52.000   108.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); CT1-CT1-C
	HAL1   CTO1   CTO1    34.500   110.10   22.53   2.179  ! lip36; alkane, 3/92; HAL1-CTL1-CTL1
	OHL    CTO1   CTO1    75.700   110.10   ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT1
	CTL2   CTO1   CTO1    52.000   108.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); CT2-CT1-C
	HAL1   CTO1   CTL2    34.500   110.10   22.53   2.179  ! lip36; alkane, 3/92; HAL1-CTL1-CTL2
	HAL2   CTL2   CTO1    26.500   110.10   22.53   2.179  ! alkane, 4/98: HAL2-CTL2-CTL1
	CTO1   CTL2   CTL2    58.350   113.50   11.16   2.561  ! glycerol; CTL1-CTL2-CTL2
	OHL    CTO1   CTL2    75.700   110.10   ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT3
	NHL    C      CTL1    80.000   116.50   ! prot22; NMA Vib Modes (LK);  NH1-C-CT1
	O      C      CTL1    80.000   121.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); O-C-CT1
	C      CTL1   CTL2    52.000   108.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C
	HAL1   CTL1   C       33.000   109.50   30.00   2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; HA-CT2-C
	OHL    CTL1   C       75.700   110.10   ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT1
	HAL1   CTO1   CTO1    34.500   110.10   22.53   2.179  ! lip36; alkane, 3/92; HAL1-CTL1-CTL1
	CTL1   CTO1   CTO1    58.350   113.50   11.16   2.561  ! glycerol 
	OHL    CTO1   CTO1    75.700   110.10   ! prot22; MeOH, EMB, 10/10/89; OH1 CT2 CT2
	O      C      CTO1    80.000   121.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); O-C-CT1
	HAL1   CTO1   C       33.000   109.50   30.00   2.16300 ! prot22; alanine dipeptide, LK, replaced, adm jr., 5/09/91; HA-CT2-C
	OHL    CTO1   C       75.700   110.10   ! prot22; MeOH, EMB, 10/10/89; OH1 CT1 CT1
	C      CTO1   CTL2    52.000   108.00   ! prot22; Alanine Dipeptide ab initio calc's (LK); CT3-CT1-C
	NHL    C      CTO1    80.000   116.50   ! prot22; Alanine Dipeptide ab initio calc's (LK); NH1-C-CT1
	!Added by Dr. Klauda and Eric for Cer6 3/17
	NHL  C    CTO1 HAL1     0.000   3     0.00 ! prot22; LK for autogenerate dihe, sp2-methyl, no dihedral potential; NH1 C CT2 HA
	NHL  C    CTO1 OHL      0.200   3     0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X; this is a stretch to tranferrability
	NHL  C    CTO1 CTL2     0.200   3     0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X
	H    NHL  C    CTO1     2.500   2   180.00 ! prot22; Gives appropriate NMA cis/trans barrier. (LK); H NH1 C CT1
	CTO1 C    NHL  CTL1     1.6000  1     0.00 ! prot22; Revised to adjust NMA cis/trans energy difference. (LK); CT1-C-NH1-CT1
	CTO1 C    NH1  CTL1     2.5000  2   180.00 ! prot22; Revised to adjust NMA cis/trans energy difference. (LK); CT1-C-NH1-CT1
	X    CTO1 CTO1 X        0.200   3     0.00 ! lip36; alkane, 3/92; X CTL1 CTL1 X
	X    CTO1 CTL2 X        0.200   3     0.00 ! lip36; alkane, 3/92; X CTL1 CTL2 X
	X    CTO1 CTO1 X        0.14    3     0.00 ! glycerol; X CTL1 OHL X
	CTO1 CTO1 OHL  HOL      5.000   1   180.00 ! torsion fit to cer6 qm, jbk 10/12
	CTO1 CTO1 OHL  HOL      0.220   2     0.00 ! torsion fit to cer6 qm, jbk 10/12
	CTO1 CTO1 OHL  HOL      1.110   3   180.00 ! torsion fit to cer6 qm, jbk 10/12
	X    CTO1 OHL  X        0.14    3     0.00 ! lipid36; glycerol; X CTL1 OHL X
	O    C    CTO1 CTL2     1.4000  1     0.00 ! par22; ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c; O-C-CT1-CT2
	O    C    CTO1 HAL1     0.00    2   180.00 ! guess
	O    C    CTO1 OHL      0.00    2   180.00 ! guess
											-> the following lines have been added from toppar_all36_lipid_sphingo.str provided by charmm-gui at http://www.charmm-gui.org/?doc=input/membrane.bilayer 
	!for TSM
	CTL1   CTO1   CTL2    52.000   108.00   ! prot22; Alanine Dipeptide ab inition calc's (LK); CT1 CT1 C


toppar_all36_lipid_sphingo.str 	 
toppar_all36_lipid_yeast_para.str 			-> toppar_all36_lipid_yeast.str without lipid topologies and with Charmm commands commented			
toppar_all36_lipid_yeast.str 	 
toppar_all36_lipid_detergent_para.str 		-> toppar_all36_lipid_detergent.str without lipid topologies					
toppar_all36_lipid_detergent.str 	 
toppar_all36_lipid_ether_para.str 			-> toppar_all36_lipid_ether_para.str 
toppar_all36_lipid_ether.str 	 

toppar_all36_carb_glycolipid_para.str 		-> toppar_all36_carb_glycolipid.str without lipid topologies			
toppar_all36_carb_glycolipid.str 		 
toppar_all36_carb_glycopeptide.str 		 
toppar_all36_carb_imlab_para.str 			-> toppar_all36_carb_imlab.str without lipid topologies			
toppar_all36_carb_imlab.str 				

toppar_all36_na_nad_ppi.str 			
toppar_all36_na_rna_modified.str 		



