<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory.</DIV>
<DIV> </DIV>
<DIV>many thanks.</DIV>
<DIV> </DIV>
<DIV>Bernard<BR><BR>--- On <B>Wed, 2/2/11, 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: Wednesday, February 2, 2011, 2:32 AM<BR><BR>
<DIV class=plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>> <BR>> this is the command i am using:<BR>> pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce<BR>> then I choose a force fileld.<BR>> then I get the error and no new files generated at all.<BR>> My working directory is:<BR>> /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests<BR>> <BR><BR>I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed? It's a bad idea to run commands from the location of the installation or its subdirectories. It's also a possibility that the space in "molecule tests" is causing problems with filename parsing, but that's a bit of a guess.<BR><BR>Move the necessary files to a new location, in a directory named without spaces, and try again.<BR><BR>-Justin<BR><BR>> --- On *Wed, 2/2/11, Justin A. Lemkul /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu"
ymailto="mailto:jalemkul@vt.edu">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" ymailto="mailto:jalemkul@vt.edu">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" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> Date: Wednesday, February 2, 2011, 2:15 AM<BR>> <BR>> <BR>> <BR>> Mr Bernard Ramos wrote:<BR>> > Hi!<BR>> > I am actually following your lysozyme tutorial. I ve been using<BR>> different pdb files including that of water, methanol, 1AKI, etc.<BR>>
The pdb2gmx does not generate any topology file. No files are<BR>> generated and I get this error:<BR>> > ------------------------------------------<BR>> > pdb2gmx, VERSION 4.5.3<BR>> > Source code file: futil.c, line:491<BR>> > File input/output<BR>> > 1AKI.pdb<BR>> > For more.... etc<BR>> > ------------------------------------------<BR>> ><BR>> <BR>> Then this file doesn't exist in the working directory. What is the<BR>> command you're issuing (exact copy and paste from the terminal,<BR>> please)? What are the contents of the working directory?<BR>> <BR>>
-Justin<BR>> <BR>> ><BR>> > --- On *Mon, 1/31/11, Mr Bernard Ramos /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com" ymailto="mailto:bgrquantum@yahoo.com">bgrquantum@yahoo.com</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com</A>>>/*<BR>> wrote:<BR>> ><BR>> ><BR>> > From: Mr Bernard Ramos <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com" ymailto="mailto:bgrquantum@yahoo.com">bgrquantum@yahoo.com</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com"
target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquantum@yahoo.com</A>>><BR>> > Subject: Re: [gmx-users] luck<BR>> > To: <A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>,<BR>> "Discussion list for GROMACS users"<BR>> > <<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://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>>><BR>> > Date: Monday, January 31, 2011, 1:14 PM<BR>> ><BR>> > thanks.<BR>> > Here is the error i mentioned a while back with<BR>> using pdb2gmx:<BR>> > ----------------------------------------------------------<BR>> > File input/output error:<BR>> > filename.pdb<BR>> > For more information, visit ............<BR>> >
----------------------------------------------------------<BR>> > thanks for the time<BR>> ><BR>> > --- On *Mon, 1/31/11, Justin A. Lemkul /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=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" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A
href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>><BR>> > Subject: Re: [gmx-users] luck<BR>> > To: "Gromacs Users' List" <<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://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>>><BR>> > Date: Monday, January 31, 2011, 12:33 PM<BR>> ><BR>> ><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<BR>> time<BR>> > and effort than simply trying it yourself ;)<BR>> ><BR>> > -Justin<BR>> ><BR>> > > --- On *Mon, 1/31/11, Justin A. Lemkul<BR>> /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu"
ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>><BR>> > <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>>/*<BR>> > wrote:<BR>> > ><BR>> > ><BR>> > > From: Justin A. Lemkul <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>>
<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>><BR>> > <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>><BR>> > > Subject: Re: [gmx-users] luck<BR>> > > To: "Discussion list for GROMACS users"<BR>> > <<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://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>><BR>> > <<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>>><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<BR>> mdrun"<BR>> > was able to<BR>> > > give the correct path, I was not able to run "luck".<BR>> > Instead, "luck"<BR>> > > gives an error "command not found". Is this ok?<BR>> What went<BR>> > 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<BR>> > structure file<BR>> > > "*.pdb" as the error. Does this in dicate that the<BR>> > program was not<BR>> > >
installed properly or there is an error with the<BR>> pdb file.<BR>> > > ><BR>> > > If the program has given you a fatal error, then the<BR>> > program is<BR>> > > correctly installed and working. It is your input<BR>> that<BR>> > is somehow<BR>> > > wrong. Without the actual error message, it's<BR>> impossible<BR>> >
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>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" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<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>><BR>> > <<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>><BR>> > > <<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>><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<BR>> > > <A
href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A><BR>> > before posting!<BR>> > > Please don't post (un)subscribe requests to the<BR>> list. Use<BR>> > the www<BR>> > > interface or send it to<BR>> <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>> <<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>><BR>> > <<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>><BR>> > > <<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>>.<BR>> > > Can't post? Read<BR>> <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>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>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" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<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>><BR>> > <<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>><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<BR>> > <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A><BR>> before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the<BR>> > www interface or send it to <A
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> -----Inline Attachment Follows-----<BR>> ><BR>> > -- gmx-users mailing list <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://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>><BR>> > <<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>><BR>> > <A href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=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>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>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>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" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <<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>><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<BR>> <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<BR>> 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>> <<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>>.<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>> <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>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" 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>