<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">If atoms are missing in the sidechains of your protein, you can try a program like scwrl3 to rebuild all or some of the sidechains. This will give you complete sidechains in sort of reasonable positions. <div><br></div><div>Cheers</div><div>/Per</div><div><br></div><div><br><div><br></div><div><br><div><div>12 aug 2008 kl. 15.04 skrev vivek sharma:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi David,<br>Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same?<br>whether swiss pdb can help in such cases?<br> <br>With Thanx,<br>Vivek<br><br><br><br><div class="gmail_quote">2008/8/12 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div><div></div><div class="Wj3C7c">vivek sharma wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Hi There,<br> <br> I am new to molecular dynamics and GROMACS.<br> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command....<br> <br> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce<br> <br> I got the following in the last of error.....<br> ......<br> ......<br> ......<br> .......<br> N-terminus: NH3+<br> C-terminus: COO-<br> WARNING: atom CE2 not found in residue 270 while adding atom<br> <br> -------------------------------------------------------<br> Program pdb2gmx, VERSION 3.3.3<br> Source code file: genhydro.c, line: 304<br> <br> Fatal error:<br> Atom CE2 not found in residue PHE270 while adding hydrogens<br> -------------------------------------------------------<br> I tried the same with different force field and water models, but getting the same error again and again.<br> any suggestion will be highly appreciated.<br> </blockquote> <br></div></div> You have an incorrect pdb file. An atom is missing. You have to fix it yourself.<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> <br> With thanx,<br> Vivek<br> <br> ------------------------------------------------------------------------<br> <br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote> <br> <br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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 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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote></div><br></div> _______________________________________________<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">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></div></body></html>