<DIV>Thanks David for you replay. Actually te ligand BZA has a charge -1 so, Do you think that it is the problem? in this case How can I improve this?. In my simulations I used RF with epsilon=78 , FF gromos 96, Coulomb radio= 1.0 and Van der Wals radio= 1.0, to measure Van der Wals energiesut-off. I used nlist=5 y rlist= 10 too. The rest of the parameters are the standars, temperature coupling and pressure coupling = berendsen.</DIV>
<DIV> </DIV>
<DIV>Thanks again</DIV>
<DIV>Cesar<BR><BR></DIV><B><I></I></B>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">On Sat, 2005-03-19 at 09:49 -0800, Cesar Lopez wrote:<BR>> Dear Gromacs users:<BR>> <BR>> I used Gromacs to repeat a simulation of the method<BR>> LIE (Peter A. Kollman 1999 ) with the Trypsin and the<BR>> Bza.<BR>> <BR>> I have obtained similar values of binding free energy,<BR>> at least using LIE method and the clasical equation,<BR>> when I analyzed the punctual energies of my sistem (<BR>> drug in water and drug in protein) I saw that the LJ<BR>> energier are very similar to the Wan der vals<BR>> aproximation that they used, but when I compare the<BR>> Coulomb energies (In Gromacs S-R Coulomb energies)<BR>> are very different, for example ,They had 114 Kcal/mol<BR>> in protein and 110 Kcal/mol in water, while I obtained<BR>> 240 and 220 KJ/mol in each case.<BR>Is this really the interaction energy? Or do you have a charged
ligand?<BR>The differences are very similar though, so somewhere there seems to be<BR>a constant energy term. How about cut-off treatment, force field...<BR><BR><BR>> <BR>> My questions are:<BR>> Can different methods obtain different coulomb<BR>> energies?<BR>> Is there any difference If I use constraints????? or<BR>> maybe cutt-offs?<BR>> Is the forcefield the guilty?<BR>> <BR>> The strange Is that I have repeated with more proteins<BR>> and the behavior is similar , differents coulomb<BR>> energies, similar LJ to the experiments, and the free<BR>> energy similar to the experimental.<BR>> Thanks for your time<BR>> Cesar <BR>> <BR>> __________________________________________________<BR>> Do You Yahoo!?<BR>> Tired of spam? Yahoo! Mail has the best spam protection around <BR>> http://mail.yahoo.com <BR>> _______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>&g
t;
http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept. of Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR></BLOCKQUOTE><p>
<hr size=1>Do you Yahoo!?<br>
<a href="http://us.rd.yahoo.com/my/navbar/sethp/*http://www.yahoo.com/r/hs
">Make Yahoo! your home page</a>