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Hi,<br><br>The issue here is not so much net neutrality of the whole system<br>(although there can be important reasons for wanted this),<br>but that your system has a small fractional charge.<br>This indicates that there a probably missing atoms, probably in your ligand.<br>That is a serious problem which you should fix.<br>Check if all atoms in your ligand are present in the topology file.<br><br>Berk<br><br>> Date: Tue, 7 Apr 2009 17:16:19 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] the reson for neutralizing the charge<br>> <br>> Homa Azizian wrote:<br>> > Hi <br>> > I have a basic question about the charge. why is it important to neutralize <br>> > the charge of ligand-protein complex. Is it true by neutralizing the tatal <br>> > charge of ligand-protein complex we prevent the electrostatic intraction of <br>> > ligand and protein?<br>> > Any suggestion would be appreciated.<br>> <br>> Physical systems are normally neutral - cells have to do work to <br>> maintain ion and/or charge imbalances.<br>> <br>> Physical models were normally parameterized under neutral conditions - <br>> but you should check the literature for your force field.<br>> <br>> Some algorithms might be doubtful under non-neutral conditions - I'm not <br>> sure whether Ewald methods are well-formed in such cases. Most <br>> derivations I've seen seem to require it.<br>> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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