HI All,
"ERROR : No.of Coordinates in Solv.gro and Topol.top not matching"
I am trying to run GROMACS simulation for Protein-Ligand complex, and I am facing this issue, and I dont know how to over come/rectify it.
I have made the Protein-Ligand complex file (gromacs structure file) and have added up the number of atoms in the complex file. I have added the 'insert DRG.itp' into the Topology file.
I tried running it with another protein file, and still the same error occurs. Please see the attached image and suggest me how to rectify this.
Does the ligand have 49 atoms? If so, you forgot to add it to [molecules] in topol.top.
No. The ligand has 83 atoms. and I have added the Ligand atoms already. This is specifically some error in the Solv atoms.
I dont have a Linux system. So, I am running Ubuntu plugin inside of Windows10 and executing GROMACS, I assume that this shouldnt be causing any problem ? But that too, this Solv is very unique, I havnt seen it before.
The underlying issue with this error is always bookkeeping, so you're not accounting for something accurately. There is a warning above the error about a non-integral charge; if it is actually a large magnitude, this could suggest other underlying issues with your system. But given the present information, there's not much to suggest other than to carefully count everything that is in the coordinate file and the topology to see where the mismatch is. There is a tutorial that walks through a protein-ligand system if you are not used to working with them: http://www.mdtutorials.com/gmx/complex/index.html
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