<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><P>Dear sir/Madam <STRONG> thanks in Advance</STRONG></P><P> i Did dos2unixconversions. as u saiid . but still i get error when i run the same output configure in command prompt of Redhat linux5 as follows</P><P></P><P>checking for a BSD-compatible install... /usr/bin/install -c<BR>checking whether build environment is sane... yes<BR>: command not foundissing: line 3: <BR>: command not foundissing: line 5: <BR>: command not foundissing: line 9: <BR>: command not foundissing: line 14: <BR>: command not foundissing: line 19: <BR>: command not foundissing: line 24: <BR>: command not foundissing: line 29: <BR>'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in<BR>'root/mopac7-1.10/missing: line 47: `case "$1" in<BR>configure: WARNING: `missing' script is too old or missing<BR>checking for gawk...
gawk<BR>checking whether make sets $(MAKE)... yes<BR>can not run ./config /bin/sh :Error<BR></P><P><STRONG>Please kindly mail me the error free configure file to My personal Email (scvsankar_agr@yahoo.com) i am expecting your positive reply if u send me the the configure file it will be very very helpful to me thanks in Advance</STRONG></P><P></P><P><BR></P><BR><P></P><P></P><P></P><P></P><P></P><P>--- On <B>Wed, 6/5/09, vidhya sankar <I><scvsankar_agr@yahoo.com></I></B> wrote:<BR></P><BLOCKQUOTE style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><BR>From: vidhya sankar <scvsankar_agr@yahoo.com><BR>Subject: RE: [gmx-users] extending simulations<BR>To: gmx-users@gromacs.org<BR>Date: Wednesday, 6 May, 2009, 8:15 PM<BR><BR><DIV id="yiv1864884072"><TABLE cellspacing="0" cellpadding="0" border="0"><TBODY><TR><TD valign="top" style="font:inherit;"><DIV><FONT face="Times New Roman"
size="3">dear sir/Madam </FONT> </DIV>
<P class="MsoNormal" style="MARGIN:5pt 0in;"><FONT face="Times New Roman" size="3">i want to work in mopac/gromacs interface for that i have downloaded mopac 7-1.10 tar.gz when run ./configure in the TAR file in command prompt of redhat linux EL5 to install mopac</FONT>
<P class="MsoNormal" style="MARGIN:5pt 0in;"><FONT face="Times New Roman" size="3"> i got the the following error in command prompt </FONT>
<P class="MsoNormal" style="MARGIN:5pt 0in;"><FONT face="Times New Roman"><B><SPAN style="FONT-SIZE:10pt;">bash: ./configure: /bin/sh^M: bad interpreter: No such file or directory</SPAN></B></FONT>
<P class="MsoNormal" style="MARGIN:5pt 0in;"><FONT face="Times New Roman"><SPAN> please kindly rectify the error in the configure file i am waiting for your reply</SPAN></FONT>
<DIV>thanks in Advance</DIV>
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<DIV><BR><BR>--- On <B>Wed, 6/5/09, kyungchan chae <I><ckcumaa@umich.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT:5px;MARGIN-LEFT:5px;BORDER-LEFT:rgb(16,16,255) 2px solid;"><BR>From: kyungchan chae <ckcumaa@umich.edu><BR>Subject: RE: [gmx-users] extending simulations<BR>To: "'Discussion list for GROMACS users'" <gmx-users@gromacs.org><BR>Date: Wednesday, 6 May, 2009, 8:02 PM<BR><BR>
<DIV class="plainMail">If you want to extend your simulation, simply use the 'append' command.<BR><BR>: mdrun -append yes -cpi state.cpt<BR><BR>Extending a simulation is quite simple. However, if your trajectory file is<BR>larger than 2GB, you are going to have a problem. I tested it a few weeks<BR>ago and found out that the 'append' option only worked when the size of<BR>trajectory file is smaller than 2GB. I reported this issue to Gromacs<BR>bugzilla(#315). Please check my bug report. I really hope to share<BR>information about this issue.<BR><BR><BR><BR>-----Original Message-----<BR>From: <A rel="nofollow" target="_blank" href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs..org</A> [mailto:<A rel="nofollow" target="_blank" href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A>]<BR>On Behalf Of Anna
Marabotti<BR>Sent: Wednesday, May 06, 2009 8:31 AM<BR>To: <A rel="nofollow" target="_blank" href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Subject: [gmx-users] extending simulations<BR><BR>Dear all,<BR>I'd need to have a clarification about how to extend a simulation made using<BR>GROMACS 4 that has been<BR>interrupted on a system due to walltime expiration. On the Wiki section I<BR>see:<BR>"A simulation that has completed is extended using tpbconv, mdrun and<BR>checkpoint files (.cpt). A simulation<BR>that has terminated, but not completed, due to e.g. the queue time ending,<BR>or better: the use of the -maxh<BR>option of mdrun, can be continued without tpbconv. First the number of steps<BR>or time has to be changed in the<BR>.tpr file, then the simulation is continued from the last checkpoint with<BR>mdrun. This will produce a binary<BR>identical simulation that will be the same as it a
continuous run was made.<BR>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<BR>mdrun -s next.tpr -cpi previous.cpt"<BR><BR>If I understand well, the procedure using tpbconv should be applied only if<BR>I have finished my previous run<BR>of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have<BR>to use tpbconv and then mdrun. On<BR>the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only<BR>command I should provide is:<BR><BR>mdrun -s previous.tpr -cpi previous.cpt<BR><BR>without modifying the previous.tpr file.<BR>Could you please confirm me about this point?<BR>Many thanks and best regards<BR>Anna<BR><BR>______________________________________________<BR>Anna Marabotti, Ph.D.<BR>Laboratory of Bioinformatics and Computational Biology<BR>Institute of Food Science, CNR<BR>Via Roma 64<BR>83100 Avellino (Italy)<BR>Phone: +39 0825 299651<BR>Fax: +39 0825 781585<BR>Skype: annam1972<BR>E-mail: <A rel="nofollow"
target="_blank" href="http://in.mc948.mail.yahoo.com/mc/compose?to=amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A><BR>Web page: <A rel="nofollow" target="_blank" href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A><BR>____________________________________________________<BR>"If you think you are too small to make a difference, try sleeping with a<BR>mosquito"<BR><BR>_______________________________________________<BR>gmx-users mailing list <A rel="nofollow" target="_blank" href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A rel="nofollow" target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A rel="nofollow" target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!<BR>Please don't post
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