Hi everyone,
I have to do Molecular dynamics of zn binding protein by gromacs5.1.4.
I found that i can use the CHARMM27 force field. But I am not able to get the tutorial for CHARMM27 for gromacs for Zn binding proteins?
Anyone please send me the link of molecular dynamics tutorial of Zn containing proteins by CHARMM27 in gromacs?
Thank you in advance.
Dear Vikram
Same Gromacs tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html) can use for your Zn binding protein. There is no any tutorial available based on type of force field.
What type of problem you are getting using CHARMM27? If you will share specific problem then I can help you in more worthwhile manner.
Regards
Nandan
Thank you Nandan Kumar.
I have zinc binding protein along with substrate analog in which zn is 2.4 A from the carbon of the ligand. I have docked some other compunds at the same position. Now i want to compare the results of substrate analog and docked compound complex structure by MD.
I have not started with CHARMM27. I just thought that may be input files like em.mdp, nvt.mdp, npt.mdp and md.mdp of GROMMOS96 43al is different then CHARMM force field.
There is no any direct link between force field and .mdp file. From the force field U r just fetching the energy potentials or parameters for your input structure and mdp file control and lead the simulations. Whatever mdp file is available in gromacs tutorial that is appropriate to start a normal simulation.
You can edit the .mdp file as per your specific needs and desires but not due to force field types.
Regards,
Nandan
Thank you Nandan.
I want to know that how we deal with Zn in this case.
i have just done MD for proteins without metal using Gromos96 43al. In that case I just make top file of ligand from prodrg and protein from GROMOS pack.
U take whole complex (protein+ligand+metal ion) as a input for pdb2gmx and whatever problem will come, let me know.
I have tried this. I got the error that Zn has not been found in residue topology database.
Please go through the given link (http://mackerell.umaryland.edu/charmm_ff.shtml) and download the "charmm36-jul2017.ff.tgz" force field file, extract it and keep it in ur working directory. At the time of pdb2gmx, u have to select 1 to select this downloaded force field.
If u r working directory is Desktop/md_simulation, U will get option like
Select the Force Field:
From 'home/username/Desktop/md_simulation/charmm36-jul2017/........../':
1: charmm36-jul2017
From '/usr/local/gromacs/share/gromacs/top':
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
May be after uaing this force field u won't get that error.
Regards
Nandan
Hi Vikram Dalal
It is true that many force field do not take into account hyperpolarizability of residues that coordinate with zinc. As such, you will be able to run the simulation of your zinc bound pdb file with CHARMM27 as well as CHARMM36 simply by changing the name of the residue ZN to ZN2; however, proceed with caution, as CHARMM36 considers only vdW and Elec. potential (non bonded interactions) for such complexes. during the course of your simulation, the zinc ion may "flip" out of the coordination site, giving you an erroneous result. I would suggest that you use GROMOS53v6 for this. I have found that its results are more in line of what you would see in your X-ray structure, and although CYS-ZN distance come out as a bit overestimated, its not significant during the course of, say, 20ns or so...
Hi again. You can also use the parameters used in the following study:
Zn Protein Simulations Including Charge Transfer and Local
Polarization Effects (J. Am. Chem. Soc., 2005, 127 (13), pp 4921–4929; DOI: 10.1021/ja0429115) and tweak the CHARMM27 or CHARMM36m ff accordingly.
Hi Arunabh,
Thank you for your suggestions.
I have done that work using GROMOS54a7FF force field in gromacs.
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