actually i am new in gromacs, i started to follow the protein ligand simulation tutorial from gromacs server, but there i cant understand how will i make the topologies from PRODRG webserver. can you please make it clear that how will i distinguish the atom types in PRODRG server resullts?
Thanks lalit, but i try to draw the attention that how can i change the charge and atom types according to that tutorial?
Dear Pal
PRODRG parameters lead to serious artifacts. Please have look at this paper
http://pubs.acs.org/doi/abs/10.1021/ci100335w
Please see the comment from Justin (Developer in Gromacs) in the link below
https://www.researchgate.net/post/Is_it_correct_to_use_PRODRG_beta_server_to_create_a_topology_file_for_use_in_Molecular_dynamics_simulation
.gro and itp file for Ligand molecule. Available from: https://www.researchgate.net/post/gro_and_itp_file_for_Ligand_molecule [accessed Jun 1, 2017].
I agree to Thirumal. Actually you need to know what suitable force fields to use for creating your topology. You should consider all hydrogens in ligand, Prodrg is not good. So, try to use charmm force fields with web server SwissParam with partial charges assigned of the force field MMFF94.
Good lock!!
okk Elias i will try....thank you. Can charm force field will not create any problem?
I use that force field when working with protein-ligand complex and the results have always been good.
Pay attention to hydrogens and partial charges!!
Don't worry!!! The procedure is the same with two ligands. You should make both topologies for ligands and then include them in your .top file
Please, to help you. You can use the method by Analyse interaction between potente inhibitors using molecular dynamics. 2015 Molecular Simulation.
Santos, E. S et. all
Elias Santos but the problem is that whenever i introduces two ligand topologies that time first ligand is accepted but whatever the second one is not accepted by showing the error notification that "invalid order for directive atomtypes".
Can you tell me the way out??
I see. The problem probably is in your topology, i.e, in the order of .itp files You must put your ligand after forcefield. So, try switching the order of the respective ligand molecules (.itp) and see whether grompp works or not.
yeah you are right. but when i put the single ligand topology after forcefield .itp files then its running, but after adding another ligand topology then the problem is actually came. so i want to know how can anyone add two or more ligand in the topology?
The gromacs has order directives. If the order of topology is wrong error appears. If you put the itp in right sequence and grompp doesnt work, i dont know what is happen. Sorry!!
Dear Sourav Pal , how do you solve this problem ? currently I have the same error in my MD system. The first ligand is recognized but no the other? Thank you in advance for you support
- Badges
- Science topic