Got it already. Thank you!! > > > On 6/27/12 4:31 AM, [email protected] wrote: >> Hi everybody, >> I am going through the tutorial for membrane protein simulation which is >> offered by gromacs. >> I did everything just like it is described in the tutorial but when I >> want >> to do the minimization in Step 3 after packing the lipids around the >> protein I always get the error the >> "number of coordinates in coordinate file (system_inflated.gro, 9900) >> does not match topology (topol.top, 3800)" >> I understand why it is like that because I just append the membrane to >> the >> protein file but how can I also change the topology file? >> > > With a text editor. The content of the [molecules] directive must always > agree > with the contents of the coordinate file, with respect to number of > molecules > and the order in which the molecules appear. You likely need to add a > line in > this directive indicating the number of DPPC molecules, which appears to > be 122 > (9900-3800 = 6100 = 122 * 50). > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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