[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
thank you for your answer. Now it worked and I could do the minimization.
But now I have the same problem again but now the difference is 630.
So what I did is that I ran the minimization and everything worked. And
than I used the
"perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat"
command of the tutorial and now I got the error:
"number of coordinates in coordinate file (system_shrink1.gro, 9220)
             does not match topology (topol.top, 9850)"
But I changed nothing at the topology file.

Bests,
Eva
>
>
> On 6/27/12 4:31 AM, reisingere at 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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