<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Hi!</DIV>
<DIV> </DIV>
<DIV>I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error:</DIV>
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<DIV>------------------------------------------</DIV>
<DIV>pdb2gmx, VERSION 4.5.3</DIV>
<DIV>Source code file: futil.c, line:491</DIV>
<DIV> </DIV>
<DIV>File input/output</DIV>
<DIV>1AKI.pdb </DIV>
<DIV>For more.... etc</DIV>
<DIV>------------------------------------------ </DIV>
<DIV><BR><BR>--- On <B>Mon, 1/31/11, Mr Bernard Ramos <I><bgrquantum@yahoo.com></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Mr Bernard Ramos <bgrquantum@yahoo.com><BR>Subject: Re: [gmx-users] luck<BR>To: jalemkul@vt.edu, "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Monday, January 31, 2011, 1:14 PM<BR><BR>
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<DIV>thanks. </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Here is the error i mentioned a while back with using pdb2gmx:</DIV>
<DIV> </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><jalemkul@vt.edu></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 <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] luck<BR>To: "Gromacs Users' List" <gmx-users@gromacs.org><BR>Date: Monday, January 31, 2011, 12:33 PM<BR><BR>
<DIV class=yiv1313076501plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>> Do I need to type in g_luck instead?<BR>> <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>> --- On *Mon, 1/31/11, Justin A. Lemkul /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank rel=nofollow>jalemkul@vt.edu</A>>/* wrote:<BR>> <BR>> <BR>> From: Justin A. Lemkul <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank rel=nofollow>jalemkul@vt.edu</A>><BR>> Subject: Re: [gmx-users] luck<BR>> To: "Discussion list for GROMACS users" <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow>gmx-users@gromacs.org</A>><BR>> Date: Monday, January 31,
2011, 12:11 PM<BR>> <BR>> <BR>> <BR>> Mr Bernard Ramos wrote:<BR>> > Hi everyone!<BR>> > I have two questions.<BR>> > 1. after I installed gromacs 4.5.3 and "which mdrun" was able to<BR>> give the correct path, I was not able to run "luck". Instead, "luck"<BR>> gives an error "command not found". Is this ok? What went wrong? Do<BR>> I need to install again gromacs?<BR>> > <BR>> The program is now called g_luck.<BR>> <BR>> > 2. I tried doing "pdb2gmx". The error points the structure file<BR>> "*.pdb" as the error. Does this in dicate that the program was not<BR>> installed properly or there is an error with the pdb
file.<BR>> > <BR>> If the program has given you a fatal error, then the program is<BR>> correctly installed and working. It is your input that is somehow<BR>> wrong. Without the actual error message, it's impossible to say<BR>> what's wrong.<BR>> <BR>> -Justin<BR>> <BR>> > Thanks<BR>> ><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 rel=nofollow>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR>> <BR>> ========================================<BR>> -- gmx-users mailing list <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow>gmx-users@gromacs.org</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow>http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>><BR>> <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank
rel=nofollow>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at<BR>> <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank rel=nofollow>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<BR>> interface or send it to <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank rel=nofollow>gmx-users-request@gromacs.org</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank rel=nofollow>http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists"
target=_blank rel=nofollow>http://www.gromacs.org/Support/Mailing_Lists</A><BR>> <BR>> <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 rel=nofollow>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank rel=nofollow>gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank rel=nofollow>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 rel=nofollow>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" target=_blank rel=nofollow>gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank rel=nofollow>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></BLOCKQUOTE></TD></TR></TBODY></TABLE><BR></DIV><BR>-----Inline Attachment Follows-----<BR><BR>
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