GROMACS 4.5 with charmm.<br><br>So one solution could be to open the output pdb file in a software like Pymol, correct the coordinates and then make changes in the .gro file? Or do I also need to edit the other files?<br><br>
Pooja <br><br><div class="gmail_quote">On Tue, Oct 26, 2010 at 1:29 AM, Pär Bjelkmar <span dir="ltr"><<a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello,<br>
<div class="im"><br>
> I use pdb2gmx command to convert a pdb file to a .gro and .top file(using<br>
> CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3.<br>
> When I use editconf to get a pdbfile from the .gro file generated, the C=0<br>
> and the NCH3 seem to clash in space in pymol.<br>
><br>
</div><div class="im">> Is there a way of correcting this?<br>
<br>
</div>this sounds fishy, might be an error in the formation of the CT3. Have to look into that. What GROMACS version are you running?<br>
<font color="#888888"><br>
/Pär Bjelkmar--<br>
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