I want to generate a top file for a MD simulation in Gromacs. I specifically want all atom topology. The ATB server indeed generated such topology, but I want to use Amber charges loaded in mol2 to be converted into a top file. I tried Topolbuild1_3 but it doesn't work for me (I could not install it on Windows). Do you have any suggestions for what I could try?
Perhaps this will help: http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
It is my understanding that ATB produces a GROMOS topology. If so, you should use GROMOS charges. Conversely, if you really want to use AMBER charges, you should obtain an AMBER topology. You cannot mix and match charges between force fields. Different force fields are based on different parameterization philosophies, and all parameters are interconnected and have to be consistent. In particular, there is often a large amount of cancellation of error between electrostatic and vdW parameters. Also, dihedral parameters around rotatable bonds are essentially correction terms for deficiencies in the 1-4 and longer-range nonbonded interactions, and are therefore invalidated by switching charge model.
Thanks Kenno,
It is clear to me now that I shouldn't mix force fields with charges. I want to know your opinion on my current problem. I am generating Conformational Ensembles of some compounds through MD in Gromacs. I have used PRODRG server to generate the .gro and .itp. The .itp file is edited manually to include ffg43a1 and converted to .top file. In latter studies I want to update the charges in .top file (actually PRODRG doesn't compute charges accurately) with correct charges. In fact I have optimized the compounds through DFT using B3LYP and AM1 basis functional and also have Mullican charges computed earlier to MD simulation. I was trying ATB as it produces all atom topologies, but now I am continuing with PRODRG topologies with your suggestion. PRODRG also produces GROMOS topology (?) with GROMOS charges. I want to know can I use gastiger charges in topology files? What is your opinion about gastiger charges, can it be a good replacement of Amber charges if the MD is done with ffg43a1 force field? I was unable to generate Amber charges (AM1-BCC) for ua topology in CHIMERA, so was trying ATB.
GROMOS is not the force feild I'm most experienced with (among other things, the UA representation is too coarse for the applications I'm interested in), but there must exist recommendations in the GROMOS community on how to obtain charges that are compatible with a given version of the GROMOS force field. If you cannot find any in the literature, ask the developers of the force field.
GROMOS parametrization relies on simply using building blocks (functional groups) that are transferable between molecules. You can piece together a molecule rather easily in most cases, and the parameters are generally pretty good (but do check carefully!). For any functional groups that are not already present in the force field, we provided some recommendations in http://pubs.acs.org/doi/abs/10.1021/ci100335w.
Heh thanks Justin. This explains the nagging feeling I had that I was missing something rather obvious...
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