Hi,<br>
you'd better protonate your protein with pdb2gmx, using the -ignh and
-arg, -his, -glu ... tags to choose the protonation of each polar
residue, then you should have no problems creating your topology file.<br>
<br>
I wish it helps,<br>
MG<br>
<br><div><span class="gmail_quote">On 1/11/06, <b class="gmail_sendername">Dhananjay</b> <<a href="mailto:dhananjay.c.joshi@gmail.com">dhananjay.c.joshi@gmail.com</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;">
Hello all,<br>
<br>
I want to perform energy minimization and not MD. <br>
A .pdb file is with me and using programme "protonate" the hydrogens has been added to it.<br>
Now I want to perform energy minimization on this file.<br>
When I tried pdb2gmx to form topology file , the programme asked to ignore hydrogens using -ignh .<br>
<br>
Will it ignore all the added hydrogens ?<br>
<br>
If I want to generate .top file incluging added hydrogens, is it possible in any way ?<br><span class="sg">
<br>
-- Dhananjay<br>
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