Hi Researchers,
I'm currently trying to generate parameters for the ligand and heme group that bind/crystallised with the protein structure. I need to know, which software or programme is the best to generate parameter for the heme group that has an iron (Fe) atom in it and to prepare them for molecular dynamic simulation using amber software.
I did try some software but that software didn't accept Fe atom. So, please suggest software that can compatible with the amber force field and accept Fe atom.
this is the type of error I got when I tried to generate parameter using playmolecule software !
Thank you in advance.
Dear Priya,
I am not sure about AMBER force field but CHARMM27 has Fe atom in the force field parameters. I have performed a simulation on CYP175A1 protein which has heme with CHARMM27 forcefield in NAMD software. You can try with CHARMM27 directly.
Hello Priya,
You can use MCPB.py in amber
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
Although, some of the parameters are already available on ATB server but in this case, based on my personal experience and the kind of treatment I received from a reviewer about the parameters for Heme group, I would suggest you to kindly find some published work from where you can get the parameters for Heme group. And also take care of the ionic state of the Fe (ferric or ferrous) while looking for parameters. Kindly check the following paper for heme parametrization:
Boubeta et al Inorg. Chem. 54 527 2015; or JACS
136, 10325 2014. (https://www.sciencedirect.com/science/article/pii/S0162013416304718)
Imon Mandal Aashish Bhatt thank you for the suggestions. really appreciate it
Hi Aashish Bhatt and researchers,
I used MCPB.py in amber as per your suggestion, but I got stuck at this point.
I used a script metalpdb2mol2.py to generate a mol2 file for it.
When I ran the following command:
metalpdb2mol2.py -i FE.pdb -o mol2 FE.mol2 -c 3
p/s: I actually included the metalpdbmol2.py script from the tutorial into my system but still, I couldn't run the command.
I got the feedback as the command not found.
I really don't know what I have left out of my steps. If you could see, please let me know what was my mistake. thank you in advance to those who can help me.
which amber tool you used in your work. if you using the amber 19 or lesser version. then you need to download the script and give the python path in your script.
Carefully read the instructions and name of the atoms.
Best Regards
https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/cns/cns_1.3/tutorial/generate/tools/toppar.html
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