The PDB coordinates are total junk and the CONECT entries specify too many bonds per atom, hence the error. If you generate a proper coordinate file, it should work (but beware PRODRG topologies - you'll need to refine them considerably after the fact).

How can I correct the PDB coordinates?

How did you generate them in the first place?

Chemical structure was taken from PubChem and I tried to generate coordinate files using ProDRG.

You need to correct the CONECT records first as they are clearly wrong. Then verify that the starting geometry is reasonable by visualizing the structure with correct connectivity.

Hi Indu,your ligand is a small molecule so you may try to draw it on PRODRG and then try to create topology files.

Thank you sir.

Hi Indu

Rajan Vyas is right but you should only use the topology files generated from prodrg server in case, If you want to simulate the protein ligand complex. Take the original co-ordinate of the ligand to form complex. Another issue may arise of No. of atoms if you proceed like this, as pro-drg server provides topology of polar hydrogen atoms. So you will be have to be careful.

Another sever you can try is ATB server (https://atb.uq.edu.au/). Here you have various option.

Thanks

But from ATB provide only .itp file and not .gro file.

Yes. If you are generating the co-ordinate by using other drawing tools and not using the original co-ordinate you should only use .itp file not the co-ordinate file.

Thanks

@ Amarjeet Kumar, if we are getting .itp file only by using ATB, then without .gro file how we can modify our conf.gro file of protein.

Hello  Anu,

I am not sure if I understand your question correctly. The basic idea of simulation is that, you furnish the co-ordinates of protein ligand in xxx.gro file (xxx = some name) and .itp file contains the parameters. You need to generate the parameter file of small molecules that is your ligand as Gromacs has no any inbuilt module to deal with these small molecule. There are many approaches that can be taken to deal with this problem. One of them is through ATB server.

Now before proceeding for parameter generation it is very important to have the optimized geometry of the small molecule you are dealing with as the geometry in the original complex may not be the optimal one. So, it is suggested to generate the optimal geometry of the small molecule and then go for charge and parameter generation. For this purpose, software like Avogadro can be used.

Now as soon as you try to optimize the geometry of the small molecule,  its co-ordinates will be changed and you can not use this co-ordinates to form the complex. So, what I do is, generate the .itp file using this optimized geometry and take the .itp file form ATB but leave the co-ordinate file. Instead I use the original co-ordinate file (that was before optimization) and check for inconsistencies in atom representation if any between the .gro and .itp file, modify it and the form the complex.

I hope this will provide some clarity.

Thanks

Thank you all for your valuable responses. Anu Manhas's question is, "Gromacs does not provide .gro file for ligand. While using ATB server, how cam we generate coordinate file of ligand i.e. .gro file."

Hi Amarjeet,

Could you explain these lines"So, what I do is, generate the .itp file using this optimized geometry and take the .itp file form ATB but leave the co-ordinate file. Instead I use the original co-ordinate file (that was before optimization) and check for inconsistencies in atom representation if any between the .gro and .itp file, modify it and the form the complex."

Apart from this I would like to ask one more query. How one can generate .gro file for the ligand as it is well established fact that gromacs cannot read the HET atom file (ligand file)?