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<br><br>> Date: Mon, 26 Jul 2010 07:26:04 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp)<br>> <br>> <br>> <br>> X Rules wrote:<br>> > Precisely,<br>> > <br>> > open your xyz.top file and search for #include "spc.itp" and replace <br>> > this line with #include "tip4p.itp"<br>> > <br>> > and you will be done with.<br>> > <br>> <br>> Not if the coordinates present are for a three-point water model, in which case <br>> the same error is occurring. If you're switching models like this, you have to <br>> re-build the system.<br><br>agreed, but I build my system entirely for tip4p, i.e adding tip4p using genbox and still my top file contains spc.itp instead of tip4p.itp (possible bug?? in 4.0.5 alteast). <br><br>> <br>> -Justin<br>> <br>> > <br>> > <br>> > > Date: Mon, 26 Jul 2010 07:00:57 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Problem in setup energy minimization <br>> > step(grompp)<br>> > ><br>> > ><br>> > ><br>> > > bipin.singh@research.iiit.ac.in wrote:<br>> > > ><br>> > > > Hi all,<br>> > > > I am facing a problem when i tried the TIP4P water model<br>> > > > for the set up of energy minimization using grompp.<br>> > > > This error did'nt occur while using the spce model.<br>> > > ><br>> > > > Fatal error:<br>> > > > number of coordinates in coordinate file (1.pdb, 31975)<br>> > > > does not match topology (1.top, 24795)<br>> > > > Please help me to rectify this problem.<br>> > > ><br>> > ><br>> > > So all you did was change the water model? That would certainly <br>> > explain it,<br>> > > since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise:<br>> > ><br>> > > <br>> > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Thanks<br>> > > > Bipin<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>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > > --<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<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>> > Hotmail is redefining busy with tools for the New Busy. Get more from <br>> > your inbox. See how. <br>> > <http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2><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>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<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 /><hr />Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. <a href='http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2' target='_new'>See how.</a></body>
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