Hello,
I want to simulate my protein-lignad complex, but there is no forcefield information cited yet for this specific protein. I'm seeking the basic criteria which is taking in consideration to select a suitable ff from enlisted forcefields in groamcs.
Thanks in advance!
Hi,
Which forcefield are you trying currently?
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: [DEPRECATED] Gromacs force field (see manual)
8: [DEPRECATED] Gromacs force field with hydrogens for NMR
9: Encad all-atom force field, using scaled-down vacuum charges
10: Encad all-atom force field, using full solvent charges
Choose the GROMOS96 53a6 force field which is the latest version of the official Gromos96 force field and press Enter.
Additionally, it is highly dependent on your protein and ligand preparation and Gromacs version. Let know what difficulty you are facing in details.
Thanks Shamsuddin,
I have used AMBER03 and CHARMm27 so far with same protein and ligand but both of them gave me different results. So, i raised the question. But Mr. Elvis mentioned that we should not compare the results achieved for same protein-ligand while using different forcefields, to be very open, i don't know, why?
Dear Amir
According to me I think that GROMOS96 53a6 force field will be promising.
Cordialy
Marius
For selecting suitable force field for protein-ligand complex, just make sure to check the literature if someone has already performed simulations on same receptor. Now as you have mentioned that there is no information cited, so proceed for more recent versions of force field like CHARMM36, AMBER f99SB-ILDN, AMBER ff12SB or GROMOS or OPLS equivalents. AMBER and CHARMM parameters take care of amino acid backbone and side chain dihedrals. Now for ligand, you cannot generate topology file in the GROMACS, you have to use some online server like PRODRG, ATB. It is better to choose ATB in comparison with PRODRG.
Please check the mentioned link on “Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations” and “Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies”
http://pubs.acs.org/doi/pdf/10.1021/ct300323g
http://pubs.acs.org/doi/pdf/10.1021/ci100335w
Hi,
You have been provided with the plenty of explanations regarding the force fields.However, it is not advisable to compare the results of the simulations obtained via different force fields because the construction of forcefields is such that it has been parameterized for the focused aim. The selection of force field is the system (objective) dependent and for that one has to dig literature or go for the benchmarking in order to check the consistency.
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