<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><P>Hi amol ,</P>
<P> actually the problem is woth your topology i.e. you need to minimize the energy of your structure. Then only you can run the mdrun. I have also faced the same problem previously.</P>
<P>Best of luck.</P>
<P>Rahul Karyappa</P>
<P>NCL, Pune<BR></P><FONT face=Arial size=2>
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<TD><B><I>-- Original Message --</I></B><BR>From: "Amol D. Atre" <ssb4@udct.org><BR>To: gmx-users@gromacs.org<BR>Date: Fri, 23 Sep 2005 12:00:17 +0530 (IST)<BR>Subject: [gmx-users] FATAL ERROR<BR><BR>Hello all,<BR><BR>While running pdb2gmx for cpeptide.pdb included in tutor/gmxdenmo folder I<BR>am getting,<BR><BR>FATAL ERROR: One of the box vectors is shorter than twice the cut-off<BR>length. Increase the box size or decrease rlist.<BR><BR>Can anybody throw some light on this?<BR>OS: Linux Fedora Core<BR><BR>Command line: pdb2gmx -f cpeptide.pdb -o conf.gro -p topol.top -i posre.itp<BR><BR>Thanking in advance.<BR><BR>Regards,<BR>Amol D. Atre.<BR>Lab No.A002,<BR>Chemical Engineering Department,<BR>Mumbai University Institute of Chemical Technology,<BR>Matunga(E), Mumbai-400019.<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<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></TD></TR></TBODY></TABLE></FONT></BODY></HTML>
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