Dear Dr.Tsjerk<br><br>I know it.I know PRODRG is not very valid for evaluating free energies(According to Dr.Justin article) too.<br>But the problem is here:<br>If I know all of hydrigenes are polar,how can I have a topology with all of them?<br>
Actually there are so many polar H in my small molecules which are not included in topology file!!<br>These can change the number of Hydrogen bonds and as a resut my binding free energy!!!<br><br><br>I want to do a new work about these,I have something excellent in my mind.<br>
I only need a topology file with all hydrogenes in 43A1 force field.<br>Is there any way(except manually adding hydrogenes)?<br>Please let me know.<br>I will present a new and excellent method instead of using PRODRG<br>
Thanks in advance<br>Mohsen<br><br><div class="gmail_quote">On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<p>Hi Mohsen,</p>
<p>So you want to have a topology with all atoms for use in a united atom force field? Seems a bit awkward... PRODRG will only include polar hydrogens, in accordance with the GROMOS force field. It won't be a particular trustworthy topology, though, but you've probably caught the words of caution expressed regularly on this list.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p></p><blockquote type="cite"><div><div></div><div class="h5">On Feb 6, 2011 9:42 AM, "mohsen ramezanpour" <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>> wrote:<br>
<br>Dear All<br><br>I want to generate a topology file in 43A1 force field for a small molecule.<br>
Of course I want one which contains all hydrogens in that.<br>PRODRG doesn't generate like this.do you know another server with these conditions?<br>
<br>Thanks in advance<br><font color="#888888">Mohsen<br>
</font><br></div></div>--<br>
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