<div dir="ltr">Hi Mark,<br>Thanks for your answer. My ultimate goal is to compare biding affinities between different ligands to the same protein using the LIE method. two things bother though; First is the relatively high electrostatic energy I got between the ligand and the solvent which is considerably higher (about 5 times higher) than the electrostatic energy between the molecule and the protein , therefore using the lie equation I got a positive delta G of binding which is obviously not correct (the LJ energy values cannot compensate for the electrostatic energy difference). Secondly, my more immediate concern is to understand why I would get a positive LJ value. <br>
<br>What do you think? <br><br>Thanks,<br>Gideon<br><br>> Hi all,<br>
><br>
> I ran g_energy in order to calculate the LJ energy between a pip2<br>
> (Phosphatidylinositol 4,5-bisphosphate) molecule and the<br>
> solvent using GROMACS 4.0.7. the pip2 molecule is very polar and the<br>
> avg. coulomb energy value I got between the ligand and solvent was ~<br>
> 3100 KJ.<br>
<br>
An equilibrated condensed-phase system of mixed positive and negative<br>
charges using a normal biomolecular force field should have negative<br>
Coulomb PE.<br>
<br>
> The solvent includes water molecules and Cl and Na ions to counter the<br>
> pip2 charge. the production run was done in npt conditions. the total<br>
> charge of the pip2 molecule is -6 e. The avg. LJ energy I got was<br>
> ~190 KJ.<br>
> I am trying make sense of this. could it be that the polar<br>
> interactions between the solvent and ligand are so strong that they<br>
> can influence a positive LJ energy?<br>
> Does anyone have any idea why this could be ?<br>
<br>
Force fields are parameterized to reproduce certain experimental or<br>
computational results, in the hope that such reproduction will permit<br>
simulations using that force field to sample similar chemical ensembles<br>
with correct frequencies. They're not parameterized such that the<br>
absolute values of any energies or energy components means anything, and<br>
one has to work hard to demonstrate anything sensible about energy<br>
differences, too. What were you hoping to observe?<br>
<br>
Mark<br clear="all"><br>-- <br><div dir="rtl"><div dir="ltr"><p>Gideon Lapidoth,</p><p>MS.c candidate</p><p>Hemi Gutman Biophysics Lab<br></p><p>Department of Biochemistry & Molecular Biology </p><p>George S. Wise Faculty of Life Sciences </p>
<p>Tel Aviv University</p><p>Israel 69978 </p><p><a href="http://ashtoret.tau.ac.il/" target="_blank"></a> </p><p>Tel: (972-3) 640-9824 <br></p><p> <br></p></div></div><br>
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