<div class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>I didn’t find ccp address in your em.mdp file. Please add ccp.exe to your folder where you will run grompp and add following sentence to em.mdp file</FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">cpp<SPAN style="mso-spacerun: yes"> </SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>cpp</FONT></div><BR><BR><B><I>leila_ayadi@lineone.net</I></B> wrote: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">I used the temp.top instead of cals.top and i found the same message :<BR>number of coordinates in coordinate file <CALS.PDB,134637>does not match<BR>topology <TEMP.TOP,0>although the temp.top is not empty.<BR>I run gromacs on windows.<BR>>-- Original Message --<BR>>Date: Sun, 2 Jul 2006 09:14:53
-0700 (PDT)<BR>>From: jahanshah ashkani <ASHKANI_2003@YAHOO.COM><BR>>Subject: Re: [gmx-users] grompp problem<BR>>To: Discussion list for GROMACS users <GMX-USERS@GROMACS.ORG><BR>>Reply-To: Discussion list for GROMACS users <GMX-USERS@GROMACS.ORG><BR>><BR>><BR>>Hi, Do you have any temp.top in your folder where you ran genbox? If is<BR>yes,<BR>>you can use it instead of cals.top.<BR>><BR>>leila_ayadi@lineone.net wrote: encountered the problem when running grompp:<BR>>Fatal error : number of coordinates in coordinate file<BR>>does not match topology<BR>><BR>><BR>>the em.mdp file is as follows :<BR>>;<BR>>; User spoel (236)<BR>>; Wed Nov 3 17:12:44 1993<BR>>; Input file<BR>>;<BR>><BR>><BR>>constraints = none<BR>>integrator = steep<BR>>nsteps = 100<BR>>;<BR>>; Energy minimizing stuff<BR>>;<BR>>emtol = 2000<BR>>emstep = 0.01<BR>><BR>>nstcomm = 1<BR>>ns_type = grid<BR>>rlist =
1<BR>>rcoulomb = 1.0<BR>>rvdw = 1.0<BR>>Tcoupl = no<BR>>Pcoupl = no<BR>>gen_vel = no<BR>><BR>><BR>><BR>>___________________________________________________________<BR>><BR>>Tiscali Broadband from 14.99 with free setup!<BR>>http://www.tiscali.co.uk/products/broadband/<BR>><BR>><BR>>_______________________________________________<BR>>gmx-users mailing list 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>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>><BR>><BR>> __________________________________________________<BR>>Do You Yahoo!?<BR>>Tired of spam? Yahoo! Mail has the best spam protection around<BR>>http://mail.yahoo.com<BR>>_______________________________________________<BR>>gmx-users mailing list
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>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><BR>___________________________________________________________<BR><BR>Tiscali Broadband from 14.99 with free setup!<BR>http://www.tiscali.co.uk/products/broadband/<BR><BR><BR>_______________________________________________<BR>gmx-users mailing list 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>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> __________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around
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