<p>Hi Mohsen,</p>
<p>Now I wouldn't want to get in the way of excellent ideas :)<br>
Check the PRODRG FAQ. It is explained there (somewhere) how to force inclusion of hydrogens.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Feb 6, 2011 11:39 AM, "mohsen ramezanpour" <<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>> wrote:<br><br>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><font color="#888888">Mohsen</font><p><font color="#500050">
On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:
>
> Hi Mohsen,
>
> So ...</font></p><br>--<br>
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