[gmx-users] Error regarding topology and coordinate files

[Justin Lemkul]

On 9/12/12 2:38 PM, Bharath K. Srikanth wrote:
> Hi
>
> I am trying to run a simulation of the self-assembly of a course-grained
> lipid bilayer using GROMACS. So far, I have made a box of DSPC lipid
> molecules (7.5 x 7.5 x 7.5, 128 molecules). I have also added water
> molecules using the genbox command (768 water molecules added), and named
> the coordinate file as waterbox.gro.
>
> For the next step, when I try to run a minimization, I get an error as
> follows:
>
> Fatal error:
> number of coordinates in coordinate file (waterbox.gro, 2560)
>               does not match topology (dspc.top, 1792)
>
> What I understood from this was that the water molecules (768 water
> molecules = 2560-1792) added by genbox had not been updated to the
> topology file. However, my topology file reads as follows:
>
> #include "martini_v2.1.itp"
> #include "martini_v2.0_lipids.itp"
>
> [ system ]
> DSPC BILAYER SELF-ASSEMBLY
>
> [ molecules ]
> DSPC 128
> ; W 768
>
> which indicates that 768 water molecules have, indeed, been added to the
> topology file- this appears to be fine. Is there anything I'm missing out
> on here?
>

The "W" line is commented out, so grompp doesn't read the fact that there are 
768 W particles at all.

-Justin

-- 
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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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