Hello Anirban,<br><br>Greetings from Pawan.<br>You can find the scripts in this webiste :<br><a href="http://wiki.gromacs.org/index.php/Membrane_Simulations">http://wiki.gromacs.org/index.php/Membrane_Simulations</a><br><br>
Regards,<br>Pawan<br><br><div class="gmail_quote">On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh <span dir="ltr"><<a href="mailto:anirbanz83@yahoo.co.in">anirbanz83@yahoo.co.in</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;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Hi ALL,<br><br>I have a built a system of protein embeded in lipid bilayer and solvated it according to the GROMACS membrane simulation tutorial. I want to delete a few water molecules that are there in the hydrophobic core of the bilayer. I deleted them manually from the .gro file and corrected the atom numbers, but still getting an error:<br>
-----------------------------------------------------------------<br>Invalid line in prt_genbox_MOD.gro for atom 73510:<br> 10.81119 10.81119 10.01306<br>-----------------------------------------------------------------<br>
<br>How can I modify the last line and get a correct .gro file by removing the unwanted waters? In the tutorial it is stated that there are some scripts to remove the unwanted waters. Can anyone provide me such a script.<br>
Any suggestion is
welcome.<br><br><br><br>Regards,<br><br><br><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><b>Anirban Ghosh</b></div><div style="color: rgb(0, 0, 191);"><b>Grade Based Engineer<br>
Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></b></div></td></tr></tbody></table><br>
<hr size="1"> Cricket on your mind? Visit the ultimate cricket website. <a href="http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com" target="_blank"> Enter now!</a><br>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>