<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>