[gmx-users] POPC: Fatal error:

[Justin Lemkul]

On 4/29/20 8:50 AM, Dutta, Kunal wrote:
> Dear Friends,
> I'm trying to learn Tutorial 2: KALP15 in DPPC
> <http://www.mdtutorials.com/gmx/membrane_protein/index.html>
> The FOLLOWING PROBLEM APPEARS:
>
> "
> GROMACS:      gmx grompp, version 2018.1
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /home/kunal/Documents/MD_Simulation/B2AR in POPC
> Command line:
> gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr
>
>
> NOTE 1 [file minim.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
> Setting the LD random seed to -2044757183
> Generated 837 of the 2346 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.1
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619)
>
>
>
> *Fatal error:number of coordinates in coordinate file (popc128a.pdb,
> 14036)             does not match topology (topol_popc.top, 17621)*
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "

Likely you have specified the wrong number of water molecules in the 
topology. Don't adhere too closely to the tutorial when using different 
coordinate files (and lipids). There are probably a different number of 
waters in the POPC system so you will have to make more adjustments to 
the topology than might be immediately apparent.

-Justin

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Justin A. Lemkul, Ph.D.
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