I want to attach a molecules with the biomolecule, but unfortunately I do not have the reasonable force field for this molecule.
Now what I tried for to get force field is as follows:
1. I tried CGenFF and got a *.str file but the data in the file is different from my input file i.e. mol2 file.
2. I tried to get force field from swissparam website and received the different file as *.par, *.top file, I tried MD on this field it runs successful, but the question is that is this correct approach?
3. I tried parameter tool available in VMD too I got some output from it too, but I am not able to connect all the information.
Any guess what to do to get accurate force field parameter for my molecule.
your suggestions are highly appreciable.
The best approach is using ParamChem using CGenFF. I don't understand the problem is; a .str and .mol2 are supposed to contain different information. The output has scores for the parameters so you have a very good quantitative metric of how reliable the parameters are and what might need further tuning. Deriving topologies for arbitrary molecules is a challenging task; most automated approaches require additional intervention unless it is a very trivial case.
Dear Justin,
I have the a.str file from CGenFF now I have to separate the information for topology and parameter file, but I am confused how to do it, I tried but I failed to do so.
One more thing I want to know that how to understand that the new force field designed is correct or not.
NAMD can read .str files directly; you shouldn't have to manipulate anything. You need a PSF for the system, but for that you can just use CHARMM-GUI, where you can supply the .str file as the parameters and topology for the ligand.
Dear Justin,
Thankyou for the reply and helpful suggestion, I tried for my molecule the same way you have described, I get some output files, but it looks like the output file have less information. For your information I am attaching the molecule and the output file from charm. please let me know where I am wrong.
If you use the "Quick MD Simulator" feature of CHARMM-GUI, it will build your system (including solvation and ions) and provide you with NAMD inputs that call all the necessary files.
The coordinate file in the .zip archive seems badly distorted; check your .mol2 for validity. If it is of poor quality, so too will be the output topology.
Dear Justin,
Now, I will explain what I had done:
1. I saved the structure in a.mol2 format of VMd and uploaded to www.cgenff.paramchem.org
2. I get out put a.str from the website with 1 penalty score above than 50 in angle and 2 in dihedrals, is it OK to use this or I have to do some thing to make it correct.
Penalties that high indicate that you definitely need to tune the parameters.
Dear Justin,
I had done what you have mentioned in your previous post, now I have a.str file and its a.psf and a.pdb file but still I dont understand the next step I am still dont get your point I am sorry for that, could you please tell me what I have to do next.
Is your molecule a ligand that will bind to some biomolecule, or is intended to be a constituent residue within that biomolecule? In your original post, the word "attach" is a bit ambiguous. The approach is not very different either way, but I need to know exactly what the situation is.
molecule will bind to some biomolecule (nucleotides) and I have to investigate the interaction analysis using simulations.
A non-covalent ligand is easy to deal with. If you're using CHARMM-GUI, upload your fully constructed system (biomolecule, ligand, solvent, ions) and the server will give you the option to incorporate parameters from ParamChem if you upload a .mol2 of the ligand. You said above you have made corrections to the ParamChem output, so incorporating those changes is easy afterwards. CHARMM-GUI will give you all of the topology and parameter files you need, as well as the NAMD inputs.
Try antechamber. It is used for creating parameters and topology files for non-standard residues like organic molecule etc.
For using AMBER force fields, antechamber is a good option, to create ligand parameters for GAFF. For the CHARMM force fields, this is not an appropriate approach.
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