<br><br><div class="gmail_quote">On Mon, May 14, 2012 at 1:51 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 14/05/2012 10:42 PM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
i run the implicit simulation with virtual sites on the hydrogen of my protein. Now I want to extract coordinates and run another simulation (in explicit solvent). Is there any way to remove those virtual sites from my gro file as VMD write the file using atoms not recognized by pdb2gmx obviously? Please, help!<br>
</blockquote>
<br></div>
If your original pdb2gmx workflow with virtual sites was recorded in a shell script you'd<br>
a) have a record for when you go to write up, and<br>
b) be able to do this change easily.<br>
<br>
As it is, a few minutes with a text editor would probably work for small systems. Alternatively<br>
<br>
grep -v MCH3 in.gro > temp.gro<br>
<br>
will remove all of the lines for virtual sites named MCH3. Do that for each type of virtual site. Adjust the count of atoms at the top of the .gro file suitably at the end.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span></blockquote><div><br>Thank you Mark!<br><br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="HOEnZb">
<div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>