Accurate calculation of entropies from MD simulations is, I think, an
unsolved problem. The quasiharmonic approximation is fairly popular,
but Michael Gilson had a recent paper showing that this has serious
problems. It sounds like you are trying to do something more along the
lines of MM-PBSA though, so you may want to look at the literature on
MM-PBSA. See especially the papers by Kollman, and there is a recent
one from the McCammon group. GROMACS, however, does not have implicit
solvent at present, so....<br>
<br>
How many compounds are you trying to calculate the binding free energy
for? You may be able to use FEP/TI in explicit solvent if you are
trying to do only a small number, but it takes a lot of effort
(computational and otherwise) to get good results with this at present.<br>
<br>
David<br>
<br><br><div><span class="gmail_quote">On 12/8/05, <b class="gmail_sendername"><a href="mailto:kruegerj@fh-bingen.de">kruegerj@fh-bingen.de</a></b> <<a href="mailto:kruegerj@fh-bingen.de">kruegerj@fh-bingen.de</a>> wrote:
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear all,<br><br>I try to calculate the free binding energy of the following pdb complex:
<br>1VFA.pdb.<br>Therefore I use the formulae:<br>deltaGcomplex =(G12-G1-G2)MM<br>+(deltaG12-deltaG1-deltaG2)solv+(G12-G1-G2)unpolar_solvation-T(S12-S1-S2)<br><br>To calculate the solvation term I used APBS (in the APBS script I subtracted the
<br>homogenous dielectricum (with epsilon = 1) from the inhomogenous dielectricum<br>(epsilon for the solvent = 80)<br><br>For the unpolar solvation term I used g_sas.<br><br>Does anyone know how to calculate the entropies? (4 different terms:
<br>translational and rotational entropies, vibrational entropiy an d<br>conformational entropie)<br>And how can I calculate the implicit solvation via MM-PBSA approach with gromacs<br>or is there another possibility to calculate this term?
<br><br>Thanks a lot for help<br><br>----------------------------------------------------------------<br>This message was sent using IMP, the Internet Messaging Program.<br><br>_______________________________________________
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