Hi. I want to do simulate via gromacs for ligand- protein complex which there is 9 ligands (three of them are seperated and six of them are connected together(picture in Add files).
when I used prodrg like gromacs tutorial (GROMACS version in the 4.5.x or 4.6.x series.)
itp file for my ligands just had 35 atoms with polar and aromatic hydrogens but in the original pdb file of ligands that I grep from protein pdb (1gyc)there are 126 atomes without hydrogens), so I doubt in accuracy this method for many ligands.
and also I tried to get an itp file from ATB , an error recorded (Found infinite path length because the graph is not connected. Only single, complete molecules can be processed.)
furthermore I tried to use CGenFF, but in step of adding ion i encountered many errors like this
ERROR 1 [file nag.prm, line 31]:
Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported.
all of the 5 ERRORS were similar for ligang.prm file.
can any one guide me how I troubleshoot this problem.?
Dear Azam Roohi
As mention in gromacs tutorial, there are some different ways for generating topology ligand.
for example, ACPYPE for Amber force filed and TopolGen or Topolbuild for OPLS force field.
I recommended for use ACPYPE due to its very user-friendly.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
you can ask if you have any questions!
best regards
Hi Azam,
It seems that your molecules are not well built, before generating the force fields with PRODRG you have to make sure that your chemical structure is correct . You can do this with Gaussview or Avogadro.
Don't use PRODRG. It is wildly inaccurate and not suitable for reliable simulations.
Repeated parameters with CGenFF indicate either your parametrizing the same dihedral multiple times (don't do this, just come up with one set of parameters) or the dihedral parameters already exist in the force field, in which case you should remove your parameters from the .prm file and use the ones in ffbonded.itp.
Dear Justin Lemkul thanks a lot for your advices. Now I have another question. For cases that we want to simulate a ligand-protein complex via Gromacs and have 9 ligands that they are the same ( but 6 of them connected together), is it proper we produce itp file for just one ligand and then to account for the fact that there is 9 new molecules in coplex.gro, we have to add it here, like so?
[ molecules ] ; Compound #mols Protein_chain_A 1 ligand 9 where I want to use cgenff or ATB server to produce itp
file for ligand, is it a proper work?
Azam Roohi I don't understand what you mean by having 9 ligands but 6 are "connected together" - if they're connected (bonded?) doesn't that mean they're different? If you just have 9 copies of the same ligand, they are by definition topologically identical and you should specify 9 copies in [molecules] - their coordinates or interactions are irrelevant to parametrization in this context.
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