<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear Vivek,</DIV>
<DIV>you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs.</DIV>
<DIV> </DIV>
<DIV>nahren<BR><BR>--- On <B>Tue, 8/12/08, vivek sharma <I><viveksharma.iitb@gmail.com></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">From: vivek sharma <viveksharma.iitb@gmail.com><BR>Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Tuesday, August 12, 2008, 6:34 PM<BR><BR>
<DIV id=yiv1582906650>
<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" target=_blank rel=nofollow>spoel@xray.bmc.uu.se</A>></SPAN><BR>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<DIV>
<DIV></DIV>
<DIV class=Wj3C7c>vivek sharma wrote:<BR>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">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="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><BR><BR>With thanx,<BR>Vivek<BR><BR>------------------------------------------------------------------------<BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" target=_blank rel=nofollow>gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank rel=nofollow>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank rel=nofollow>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 rel=nofollow>gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A
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