Performance of the general amber force field in modeling aqueous POPC membrane bilayers Export

@article{citeulike:1413339, abstract = {The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m-1 per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling. {\copyright} 2007 Wiley Periodicals, Inc. J Comput Chem, 2007}, address = {Department of Chemistry and Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary; Institute of Pharmacodynamics and Biopharmacy, University of Szeged, E\"{o}tv\"{o}s u. 6, H-6720 Szeged, Hungary; Institute of Pharmaceutical Chemistry, University of Szeged, E\"{o}tv\"{o}s u. 6, H-6720 Szeged, Hungary}, author = {J\'{o}j\'{a}rt, Bal\'{a}zs and Martinek, Tam\'{a}s A.}, citeulike-article-id = {1413339}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20748}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17431937}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17431937}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/114209721/ABSTRACT}, day = {12}, doi = {10.1002/jcc.20748}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {amber, popc}, month = {April}, number = {12}, pages = {2051--2058}, posted-at = {2007-11-09 15:31:37}, priority = {2}, title = {Performance of the general amber force field in modeling aqueous POPC membrane bilayers}, url = {http://dx.doi.org/10.1002/jcc.20748}, volume = {28}, year = {2007} }

TY - JOUR ID - citeulike:1413339 L3 - citeulike-article-id:1413339 N2 - The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m-1 per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 IS - 12 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Chemistry and Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary; Institute of Pharmacodynamics and Biopharmacy, University of Szeged, Eötvös u. 6, H-6720 Szeged, Hungary; Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, H-6720 Szeged, Hungary EP - 2058 TI - Performance of the general amber force field in modeling aqueous POPC membrane bilayers VL - 28 SP - 2051 KW - amber KW - popc AU - Jójárt, Balázs AU - Martinek, Tamás PY - 2007/04/12/ UR - http://dx.doi.org/10.1002/jcc.20748 ER -