# DNA-Ligand simulation :number of coordinates doesnot match

**URL:** <https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683>\
**Category:** User discussions\
**Created:** [August 18, 2020, 3:17pm UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683 "2020-08-18T15:17:09Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![lcd](https://avatars.discourse-cdn.com/v4/letter/l/a587f6/32.png) [@lcd](https://gromacs.bioexcel.eu/u/lcd)\
**Post date:** [August 18, 2020, 3:17pm UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683/1 "2020-08-18T15:17:09Z")

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GROMACS version:5.1.1  
GROMACS modification: No  
Here post your question  
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/1ed--LGiGr4kF8hUvsoJvDvkyv99KV6fD/view?usp=sharing)  
[https://drive.google.com/file/d/1rwMZR26w1i2E9KHF4wlUOnLA8SP-\_Ffx/view?usp=sharing](https://drive.google.com/file/d/1rwMZR26w1i2E9KHF4wlUOnLA8SP-_Ffx/view?usp=sharing)

Best  
Dong

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [August 18, 2020, 3:33pm UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683/2 "2020-08-18T15:33:43Z")

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

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<div class="post-metadata">

**Author:** ![lcd](https://avatars.discourse-cdn.com/v4/letter/l/a587f6/32.png) [@lcd](https://gromacs.bioexcel.eu/u/lcd)\
**Post date:** [August 18, 2020, 4:14pm UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683/3 "2020-08-18T16:14:20Z")

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Dear Dr. Lemkul,

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

Sorry for the inconvenience.

Best  
Dong

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [August 18, 2020, 4:41pm UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683/4 "2020-08-18T16:41:58Z")

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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.

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<div class="post-metadata">

**Author:** ![lcd](https://avatars.discourse-cdn.com/v4/letter/l/a587f6/32.png) [@lcd](https://gromacs.bioexcel.eu/u/lcd)\
**Post date:** [August 19, 2020, 10:04am UTC](https://gromacs.bioexcel.eu/t/dna-ligand-simulation-number-of-coordinates-doesnot-match/683/5 "2020-08-19T10:04:12Z")

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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