Dear researchers,
I am new to Molecular dynamics.
I would like to do protein-ligand molecular dynamics by using gromacs.
My ligand is goniothalamin and my protein is PDB id 2c56 protein.
I would like to generate the topology of the ligand using CGenFF server. But I found out that my penalty score is quite high.
I cannot go to the next step of molecular dynamic as the penalty score quite high and get error.
I tried software Avogrado, but the penalty value still remain the same.
Anyone can suggest me any open server or free online webserver to solve this problem?
Thanks a lot!
I'd recommend using another force field such as CHARMM 36. In that case, you can try generating the topology using SwissParam (https://www.swissparam.ch/). If you use Amber03, you can try the Acepype server to generate the ligand topology.
Also, I recommend that you download your ligand structure from ZINC or PubChem rather than DrugBank.
Why is the penalty score high? Which part of the parametrization process contributes most to the penalty score?
Mayur Mukhi, the conformer provided by Leong Chee Yan is identical to PubChem's.
https://pubchem.ncbi.nlm.nih.gov/compound/6440856
Martin Klvana I am not very sure regarding the parameterization process. However, as I recommended, you could use a different force field as the parameterization process for some force fields can better process certain ligands (purely based on experience. For example, my FAD ligand was more easily processed for CHARMM than for AMBER03).
Martin Klvana,
I use cgenff to covert mol2 file to str file.
https://cgenff.umaryland.edu/initguess/
After I converted the file, str file was open.
Based on the Str file, I have no idea which is my penalty score in the str file.... Can you show to me?
In addition, Based on my penalty score, do I need to do any modification such as reparametrization?
Thank you.
Mayur Mukhi I follow your method to use SwissParam, and found out that there are many output files. May I know which file is the correct file that I should use? Thanks
Mayur Mukhi I cant find .tpr file...
only .crd, .ipt, .mol2, .par, .pdb, .psf, .rtf files are available....
You can combine the ligand pdb file with protein pdb file and then together convert it to .gro file to generate complex.gro. Conversely, you can convert both pdb files to .gro (using gmx editconf) and then combine both .gro files to create a complex.gro file.
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