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====== Phospholipids ======

The following charge parameters for 12 distinct phospholipids were determined, following an AMBER compatible approach. These parameters were validated by building a bilayer system for each phospholipid type and by comparing structural and dynamical values with experimental data available. When considering the DOPC phospholipid a good correlation with experimental available data was obtained. For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn<sub>1</sub>/sn<sub>2</sub>), and parameter files are presented. In addition, the values for volume per lipid (V<sub>L</sub>), area per lipid (A<sub>L</sub>), and bilayer thickness (D<sub>HH</sub>) in a bilayer setting are given, together with experimental data (when available). For the DOPC phospholipid, order parameters for the acyl chains are displayed and compared with experiment. These parameters were obtained under the General Amber Force Field (GAFF) terminology and general parameters. 

{{ mm:parameters:lipids:docmem.png?200 }}

----


===== Phosphatidylcholines (PC) =====


==== DOPC ====
//1,2-dioleoyl-sn-glycero-3-phosphocholine//

|  {{ mm:parameters:lipids:dopc.png?60 }}  |  Name  |  //1,2-dioleoyl-sn-glycero-3-phosphocholine//  |||
| ::: |  4-Letter code  |  DOPC  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  18:1(Δ<sup>9</sup>)/18:1(Δ<sup>9</sup>)  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:doc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:doc_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  1292 ± 2  |  1303  |  [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] \\ [[http://www.ncbi.nlm.nih.gov/pubmed/16604469|Kučerka, 2005]] \\ [[http://www.cell.com/biophysj/abstract/S0006-3495(08)78383-8|Kučerka, 2008]]    |
| ::: |  //A<sub>L</sub>//  |  66 ± 1.2  |  72.5, 72.4, 67.4  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  39 ± 0.3  |  36.9, 36.7  |  :::  | 
|  {{ mm:parameters:lipids:scd_doc.png?450 }}  |||||

==== DLPC ====
//1,2-dilauroyl-sn-glycero-3-phosphocholine//

|  {{ mm:parameters:lipids:dlpc.png?70 }}  |  Name  |  //1,2-dilauroyl-sn-glycero-3-phosphocholine//  |||
| ::: |  4-Letter code  |  DLPC  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  12:0/12:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dlc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dlc_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  927 ± 2  |  991  |  [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305359/|Kučerka, 2005]]  |
| ::: |  //A<sub>L</sub>//  |  45 ± 0.8  |  63.2, 60.8  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  39 ± 0.2  |  30.8  |  :::  |


==== DMPC ====
//1,2-dimyristoyl-sn-glycero-3-phosphocholine//

|  {{ mm:parameters:lipids:dmpc.png?70 }}  |  Name  |  //1,2-dimyristoyl-sn-glycero-3-phosphocholine//  |||
| ::: |  4-Letter code  |  DMPC  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  14:0/14:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dmc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dmc_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  1023 ± 2  |  1101  |  [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] \\ [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305359/|Kučerka, 2005]] \\ [[http://www.ncbi.nlm.nih.gov/pubmed/21819968|Kučerka, 2011]]  |
| ::: |  //A<sub>L</sub>//  |  53 ± 0.8  |  59.6, 59.9, 60.6  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  38 ± 0.2  |  36.0, 35.3  |  :::  | 

==== DPPC ====
//1,2-dipalmitoyl-sn-glycero-3-phosphocholine//

|  {{ mm:parameters:lipids:dppc.png?65 }}  |  Name  |  //1,2-dipalmitoyl-sn-glycero-3-phosphocholine//  |||
| ::: |  4-Letter code  |  DPPC  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/16:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dpc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dpc_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  1123 ± 2  |  1232, 1229, 1144  |  [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] \\ [[http://www.cell.com/biophysj/abstract/S0006-3495(08)78383-8|Kučerka, 2008]]  |
| ::: |  //A<sub>L</sub>//  |  51 ± 0.7  |  64.0, 63.1, 47.9  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  44 ± 0.2  |  38.0, 38.3, 44.2  |  :::  | 


==== POPC ====
//1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine//

|  {{ mm:parameters:lipids:popc.png?60 }}  |  Name  |  //1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine//  |||
| ::: |  4-Letter code  |  POPC  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/18:1(Δ<sup>9</sup>)  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:poc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:poc_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  1224 ± 2  |  1256  |  [[http://www.ncbi.nlm.nih.gov/pubmed/16604469|Kučerka, 2005]]  |
| ::: |  //A<sub>L</sub>//  |  52 ± 1.0  |  68.3, 64.3  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  46 ± 0.3  |  37.0  |  :::  | 


==== PLPC ====
//1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine//

|  {{ mm:parameters:lipids:plpc.png?60 }}  |  Name  |  //1-palmitoyl-2-linoleoyl-sn-glycero-phosphocholine//  ||
| ::: |  4-Letter code  |  PLPC  ||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/18:2(Δ<sup>9,12</sup>)  ||
| ::: |  parameters  |  {{ mm:parameters:lipids:plc_frcmod.zip | frcmod }} {{ mm:parameters:lipids:plc_prepc.zip | prepc }}  |  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  |||
| ::: |  //Value//  |  //MD ± σ / Å//  ||
| ::: |  //V<sub>L</sub>//  |  1226 ± 3  ||
| ::: |  //A<sub>L</sub>//  |  55 ± 1.2  ||
| ::: |  //D<sub>HH</sub>//  |  44 ± 0.4  || 


===== Phosphatidylethanolamines (PE) =====


==== DLPE ====
//1,2-dilauroyl-sn-glycero-3-phosphoethanolamine//

|  {{ mm:parameters:lipids:dlpe.png?70 }}  |  Name  |  //1,2-dilauroyl-sn-glycero-3-phosphoethanolamine//  |||
| ::: |  4-Letter code  |  DLPE  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  12:0/12:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dle_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dle_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  854 ± 2  |  907, 863  |  [[http://www.ncbi.nlm.nih.gov/pubmed/11063882|Nagle, 2000]] \\ [[http://www.ncbi.nlm.nih.gov/pubmed/3768325|McIntosh, 1986]]  |
| ::: |  //A<sub>L</sub>//  |  40 ± 0.4  |  51.2, 41.0  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  40 ± 0.1  |  35.6, 33.0, 39.8  |  :::  |


==== DMPE ====
//1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine//

|  {{ mm:parameters:lipids:dmpe.png?70 }}  |  Name  |  //1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine//  |||
| ::: |  4-Letter code  |  DMPE  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  14:0/14:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dme_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dme_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |||
| ::: |  //V<sub>L</sub>//  |  961 ± 2  |||
| ::: |  //A<sub>L</sub>//  |  44 ± 0.7  |||
| ::: |  //D<sub>HH</sub>//  |  42 ± 0.1  ||| 


==== DPPE ====
//1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine//

|  {{ mm:parameters:lipids:dppe.png?70 }}  |  Name  |  //1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine//  |||
| ::: |  4-Letter code  |  DPPE  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/16:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dpe_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dpe_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |||
| ::: |  //V<sub>L</sub>//  |  1066 ± 3  |||
| ::: |  //A<sub>L</sub>//  |  44 ± 0.5  |||
| ::: |  //D<sub>HH</sub>//  |  47 ± 0.3  ||| 

==== DSPE ====
//1,2-distearoyl-sn-glycero-3-phosphoethanolamine//

|  {{ mm:parameters:lipids:dspe.png?65 }}  |  Name  |  //1,2-distearoyl-sn-glycero-3-phosphoethanolamine//  |||
| ::: |  4-Letter code  |  DSPE  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  18:0/18:0  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:dse_frcmod.zip | frcmod }} {{ mm:parameters:lipids:dse_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |||
| ::: |  //V<sub>L</sub>//  |  1162 ± 3  |||
| ::: |  //A<sub>L</sub>//  |  43 ± 0.3  |||
| ::: |  //D<sub>HH</sub>//  |  52 ± 0.2  ||| 

==== POPE ====
//1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine//

|  {{ mm:parameters:lipids:pope.png?65 }}  |  Name  |  //1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine//  |||
| ::: |  4-Letter code  |  POPE  |||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/18:1(Δ<sup>9</sup>)  |||
| ::: |  parameters  |  {{ mm:parameters:lipids:poe_frcmod.zip | frcmod }} {{ mm:parameters:lipids:poe_prepc.zip | prepc }}  ||  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  ||||
| ::: |  //Value//  |  //MD ± σ / Å//  |  //Experimental / Å//  |  //Reference (Exp.)//  |
| ::: |  //V<sub>L</sub>//  |  1149 ± 3  |  1185  |  [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302872/|Rappolt, 2003]]  |
| ::: |  //A<sub>L</sub>//  |  46 ± 0.6  |  61.0  |  :::  |
| ::: |  //D<sub>HH</sub>//  |  48 ± 0.3  |  39.0  |  :::  | 

==== PLPE ====
//1-palmitoyl-2-linoleoyl-sn-glycero-phosphoethanolamine//

|  {{ mm:parameters:lipids:plpe.png?65 }}  |  Name  |  //1-palmitoyl-2-linoleoyl-sn-glycero-phosphoethanolamine//  ||
| ::: |  4-Letter code  |  PLPE  ||
| ::: |  sn<sub>1</sub>-sn<sub>2</sub>  |  16:0/18:2(Δ<sup>9,12</sup>)  ||
| ::: |  parameters  |  {{ mm:parameters:lipids:ple_frcmod.zip | frcmod }} {{ mm:parameters:lipids:ple_prepc.zip | prepc }}  |  [[#references | [Coimbra, 2013]]]  |
| ::: |  **Validation**  |||
| ::: |  //Value//  |  //MD ± σ / Å//  ||
| ::: |  //V<sub>L</sub>//  |  1152 ± 2  ||
| ::: |  //A<sub>L</sub>//  |  48 ± 0.5  ||
| ::: |  //D<sub>HH</sub>//  |  46 ± 0.3  || 

===== References =====
Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. [[http://www.tandfonline.com/doi/abs/10.1080/07391102.2012.750250?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed#.UfAXYY1wrt4 | Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless
ensemble]] . //J. Biomol. Struct. Dyn.//, **2013**
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