<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>thanks. </DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>Here is the error i mentioned a while back with using pdb2gmx:</DIV>
<DIV>&nbsp;</DIV>
<DIV>----------------------------------------------------------</DIV>
<DIV>File input/output error:</DIV>
<DIV>filename.pdb</DIV>
<DIV>For more information, visit ............ </DIV>
<DIV>---------------------------------------------------------- <BR></DIV>
<DIV>thanks for the time </DIV>
<DIV><BR>--- On <B>Mon, 1/31/11, Justin A. Lemkul <I>&lt;jalemkul@vt.edu&gt;</I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul &lt;jalemkul@vt.edu&gt;<BR>Subject: Re: [gmx-users] luck<BR>To: "Gromacs Users' List" &lt;gmx-users@gromacs.org&gt;<BR>Date: Monday, January 31, 2011, 12:33 PM<BR><BR>
<DIV class=plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>&gt; Do I need to type in g_luck instead?<BR>&gt; <BR><BR>Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;)<BR><BR>-Justin<BR><BR>&gt; --- On *Mon, 1/31/11, Justin A. Lemkul /&lt;<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>&gt;/* wrote:<BR>&gt; <BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;From: Justin A. Lemkul &lt;<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>&gt;<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Subject: Re: [gmx-users] luck<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;To: "Discussion list for GROMACS users" &lt;<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>&gt;<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Date: Monday,
 January 31, 2011, 12:11 PM<BR>&gt; <BR>&gt; <BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Mr Bernard Ramos wrote:<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; Hi everyone!<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&nbsp; I have two questions.<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&nbsp; 1. after I installed gromacs 4.5.3 and "which mdrun" was able to<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;give the correct path, I was not able to run "luck". Instead, "luck"<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;gives an error "command not found". Is this ok? What went wrong? Do<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;I need to install again gromacs?<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;The program is now called g_luck.<BR>&gt; <BR>&gt;&nbsp; &nbsp; &nbsp; &gt; 2. I tried doing "pdb2gmx". The error points the structure file<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;"*.pdb" as the error. Does this in dicate that the program was not<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;installed properly or there is an error
 with the pdb file.<BR>&gt;&nbsp; &nbsp; &nbsp; &gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;If the program has given you a fatal error, then the program is<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;correctly installed and working.&nbsp; It is your input that is somehow<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;wrong.&nbsp; Without the actual error message, it's impossible to say<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;what's wrong.<BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;-Justin<BR>&gt; <BR>&gt;&nbsp; &nbsp; &nbsp; &gt;&nbsp; Thanks<BR>&gt;&nbsp; &nbsp; &nbsp; &gt;<BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;-- ========================================<BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Justin A. Lemkul<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Ph.D. Candidate<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;ICTAS Doctoral Scholar<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;MILES-IGERT Trainee<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Department of Biochemistry<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Virginia Tech<BR>&gt;&nbsp;
 &nbsp;&nbsp;&nbsp;Blacksburg, VA<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;jalemkul[at]vt.edu | (540) 231-9080<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;<A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR>&gt; <BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;========================================<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;-- gmx-users mailing list&nbsp; &nbsp; <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>&gt;<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;<A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>&gt;&nbsp;
 &nbsp;&nbsp;&nbsp;Please search the archive at<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;<A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Please don't post (un)subscribe requests to the list. Use the www<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;interface or send it to <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;&lt;<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>&gt;.<BR>&gt;&nbsp; &nbsp;&nbsp;&nbsp;Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR>&gt; <BR>&gt; <BR><BR>--
 ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list&nbsp; &nbsp; <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/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="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></BLOCKQUOTE></td></tr></table><br>