Do you know what specific ligand you're looking at? I just went about doing some editing when I had a novel ligand. It seriously just depends on the situation. The GROMACS manual has some instruction on it. [Putting in the necessary force-field parameters, etc.] You'll need to edit your favorite force-field as well [make a duplicate] to include the parameters for the novel ligand. I still feel that just doing it manually is the way to go when it comes to novel ligands, especially if it's your first time dealing with it.

(Looking at):

http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html

Also, this is a good question to throw out @ the GROMACS mailing list: http://lists.gromacs.org/mailman/listinfo/

Thanks Jonathan. I also googled the GROMACS mailing list but no significant ans is there. I know my problem is not unique but dont know why it is un-addressed till. Well can u suggest me some thumb rule like stuff for manual topology generation. Due to confidentiality i can not revel my ligand structure here.

Is the peptide cyclic? Be sure to attach the ends together. If there's disulfide bridges [CYS-CYS], make sure you have the covalent bonds between them. Also, be sure to include the Leonard-Jones interactions. These are some rules of thumbs, but there also should be some info @ the mail-list if you do a search there.

Hello Rajnikant,

Yes, there is a server that does that and here is the link.

http://compbio.biosci.uq.edu.au/atb/

It's pretty easy to use and with it you will have all the GROMOS forcefield files you need for your simulation.

However, as Jonathan Reyles pointed out, it's not a bad idea to manually write the topology files. I do it all the time, and in fact I feel more comfortable manually writing my topologies since it makes debugging a lot easier for me. In addition it helps you understand the file structure better (Gromacs, Charmm...whichever potential you employ).

Hope this helps.

Hello all,

I was trying to parametrize the ligand molecule that I am working with which is bound to the protein covalently, but I dont know how to do it. I have been searching for it but I could not find any answer. I know I can get the topology of the ligand from servers like PRODG of ATB, but as it is now covalently bound to the protein I don`t know how to deal with it. Olujide and Jonathan, you had written here that you do yourself manually. Is there anyway that you can briefly explain or any tutorial that can help me with this? Thanks in advance.

You probably have solved the problem; sorry it has taken me this long to respond. It would have been helpful if you had provided the forcefield you're using. But then parameterising a novel group for MD takes similar form for the different forcefields. I will recommend the tutorial by the Luthey-Schulten Group "Parameterizing a novel residue."

If you already have parameters for the ligand, then you are in luck and all you need to do is to generate parameters for the 'new' connection (I refrain from using the word bond since the required parameters are not likely to be limited to bond length) between the ligand and the amino acid residue. In addition, do not forget to check if the parameters for the 'new' connection already exist in the forcefield files: this will save you a lot of trouble. Otherwise, you will need to perform QM calculations for them.

Hope this helps.

Hello all,

@Olujide Oludayo Olubiyi & @Jonathan Reyles, Is there a tutorial giving a basic guidelines about how to write a topology file.

Thanks.

sorry why we need to do topology ?