I am facing problem with MD of protein containing sugars i.e. post transitionally modified protein. This may be due to the absence of forcefield parameters for carbohydrated in MDWEB online web server.
Kindly hepp me to solve this problem.
Hi Indu,
yes, it can be due to the needed parameters. Please take a look at how to add missing parameters in MDWeb here: http://mmb.irbbarcelona.org/MDWeb/help.php?id=checkingLig
If you can tell me the PDB and modified residue codes or just send me the structure, I will try to help you during the process.
Thanks for using our portal!
Good evening,
Thank you for your quick reply. I am sending the files. Please check them. The PDB id of the protein is 3OSK and I am not able to upload modified PDB which contain sugar moiety attached to protein as these are in .pdb format. Can you suggest me some other mail on which I can send you the modified file.
Hi Indu,
I was able to open the file you sent me, and I saw the glycans attached to the protein. I’m affraid to tell you MDWeb didn’t integrate the amber glycam parameters (http://glycam.org/docs/forcefield/parameters-energy-functions/), for different reasons, mainly for the possible atom types incompatibilities with force field versions (please see http://glycam.org/docs/help/2014/07/02/which-protein-force-fields-are-compatible-with-glycam/).
Anyway, I think you were considering using the Coarse-grained methods integrated in MDWeb to obtain dynamic properties of the system, and I have to tell you that all our methods (NMA, DMD, BD) are just working with standard residues, almost all of them with just C-alpha atoms, so even with the right parameters, our CG methods wouldn’t work for your particular problem.
I’m really sorry for that. Thanks for your interest in our tool.