DNA-Ligand simulation :number of coordinates doesnot match

User discussions
1

GROMACS version:5.1.1
GROMACS modification: No
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Dear Gromacs users.

I’m running a simulation of DNA-Ligand by Gromacs. The topology file, .itp, of the ligand was prepared by Antechamber and then it was integrated into the topol.top in combination with DNA parameters. The total number of atoms in .gro was also updated.

When I ran the command :
gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr

The Graomacs gives Fatal error:
number of coordinates in coordinate file (complex_solv.gro, 8289)
does not match topology (topol.top, 8356)

It looks that the the ligand is missed in complex_solv.gro. Whereas after checking the complex_solv.gro, all the atoms of the ligand has been these.

I’m not sure what’s wrong and would you please give any suggestions?

Thanks in advance.

The ligand topology file and topol.top are here:
https://drive.google.com/file/d/1ed--LGiGr4kF8hUvsoJvDvkyv99KV6fD/view?usp=sharing
https://drive.google.com/file/d/1rwMZR26w1i2E9KHF4wlUOnLA8SP-_Ffx/view?usp=sharing

Best
Dong

2

Your links are not accessible so we can’t see the files.

3

Dear Dr. Lemkul,

The link should be accessible now and please have a look.

Sorry for the inconvenience.

Best
Dong

4

You’re double-counting the ligand. DRG.itp has a [molecules] directive with “DRG 1” and then you have “DRG 1” in topol.top, so the net effect is your topology specifies two ligands. You should only ever have one [molecules] directive in a system topology.

5

Dear Dr. Lemkul,

That’s the problem and it has been solved by changing the number of #mols to 0 in DRG.itp file.
Thank you very much.

Best
Dong