Dear researchers,
I've encountered a problem which I don't know how to find a solution for it.
Currently I'm working with NAMD package and in one of the official tutorials, I realized that the CHARMM27 is being used (this file: par_all27_prot_lipid.prm) then I wanted to change it to CHARMM36 but I couldn't find any file like this: par_all36_prot_lipid.prm.
In the toppar directory. It has these files in it:
par_all36_prot.prm
par_all36_lipid.prm
...
...
.
1- If I want to use proteins and lipid at the same time how can I use it?
2- Does CHARMM27 still a valid force field?
3- What are the differences between these versions?
4- How can I decide between force fields (CHARMM, AMBER, ...)
Thank you so much
#forcefields #NAMD #CHARMM #AMBER #topology #parameters #proteins #lipids
Here you can find different prm for CHARMM36/22: http://mackerell.umaryland.edu/charmm_ff.shtml
A little note. There is not CHARMM27 Force Field, there is only CHARMM22 and CHARMM36. CHARMM27 is a strange naming for CHARMM22.
1. Try this: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2449.html
2. There is not such FF.
3. Most likely parameters. I can't find what exactly, but if i do i will write it here.
4. Look for comparisions in publications, for example: [1].
[1] Yuguang ,Daniil S. Kosov, andGerhard Stock. Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments. J. Phys. Chem. B, 2003, 107 (21), pp 5064–5073 DOI: 10.1021/jp022445a Publication Date (Web): May 2, 2003.
@Daniel, to clarify - there is a CHARMM27 force field, but not for proteins. C27 pertains to nucleic acids and lipids. The protein force field C22 was revised at the same time to include CMAP corrections and was bundled together with the C27 release (versioning based on the CHARMM program version with which the force field was released). So there is always some confusion. The parameters in the (unfortunately named) par_all27_prot.prm file are properly referred to as CHARMM22/CMAP, not CHARMM27. But CHARMM27 (C27) is a perfectly valid indicator for nucleic acids or lipids in that version of the force field.
The differences in C36 vs. C27(C22/CMAP for proteins) are well documented in the literature. One should use C36 for everything as the lipid parameters are vastly better and the proteins are similarly improved (using the latest C36m parameters is advised if there are disordered regions in the protein).
Relevant literature:
Proteins:
dx.doi.org/10.1021/ct300400x
dx.doi.org/10.138/nmeth.4067
Lipids:
dx.doi.org/10.1021/jp101759q
dx.doi.org/10.1021/jz200167q
dx.doi.org/10.1021/jp304056p
Force field comparisons are abundant in the literature, and it is up to the user to do his/her proper homework. The choice of a force field will influence EVERY result of a simulation, so investing proper time now in making a wise choice will save a lot of (potentially) wasted effort down the road.
Thank you so much for your help. I will read the literature. The second link in proteins section doesn't work (dx.doi.org/10.138/nmeth.4067), could you write the name of article to me please?
And is it possible to tell me how can I use CHARMM36 instead of 27? Because I couldn't find any replacement for par_all27_prot_lipid.prm in CHARMM36. The Lipids and Proteins are not in the same file (par_all36_prot.prm, par_all36_lipid.prm) and in my system I have both lipids and proteins. Should I combine them in one file in some way?
Thanks again.
dx.doi.org/10.1038/nmeth.4067
You don't need to combine anything. Just use par_all36_lipid.prm and par_all36_prot.prm (or par_all36m_prot.prm to use C36m). NAMD lets you specify however many parameter files you want. Or just build the whole system with CHARMM-GUI and it will literally do everything for you, including providing you with correct input files.
John King do you mean 53A6 or 54A7? There is no 53A7 as far as I know. I personally have grown to distrust GROMOS force fields because their parametrization details are not well described in publicly available literature and what I have seen recently of validation is not particularly convincing of their quality, despite some studies (including my own) suggest they may behave well for certain systems.
In any case, I would use CHARMM36m since it was specifically calibrated for intrinsically disordered proteins and peptides, which is what I presume would be the dominant state for a 10aa peptide, but length alone can't tell you what you should choose as the force field model.
Both yield provably correct NVT ensembles; they are in no way tied to the choice of force fields.
Hi Justin, Could you please let me know if i can use charmm36 for an IDP-lipid membrane interaction?
The C36 protein force field has been recently revised to better model disordered proteins; the files are top_all36_prot.rtf and par_all36m_prot.prm (note the added 'm' in all36m).
Dear Dr. Justin Lemkul ,
I would like to do the Gromacs dynamics for the membrane protein-ligand complex. I have evaluated the protein stability with membrane using Gromos96 54A7, but I have used charmm36 all-atom force field for the protein-ligand simulation. Both the analyses are done by the different force field. So, How can I perform dynamics study for the protein-ligand complex with lipid bilayer membrane?
Kindly inform your suggestion please.
Thanks in advance.
Rajesh
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