On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de 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
========================================
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