GROMACS version:2020-5
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Here post your question
I have to simulate Cytochrome C with HEME group. I am trying using force-filed charmm36-feb2021. However, gmx pdb2gmx fails because it can’t, because it can not fix HEME group. The merged.rtp has parameters for Heme still it is not working.
Can some expert help me to fix this problem.
Best regards
Surya
Have you fixed this problem?
yes I could that. I shall be more than happy to help (if needed)
I would greatly appreciate it if you could share your approach to this issue, as I’ve been struggling with it for quite some time.
I assume you are using CHARMM-36, to parameterise your system?
Did you check the PDB how HEME entry is written in PDB file?
e.g. It was HEM instead of HEME for the case I was trying to work on.
If you have already fixed this issue, please share exact error screen shot so I can look into it.
In my case, it was HEC rather than HEM or HEME. I used CHARMM-36 to parameterise your system initially, but I changed to amber14sb. I used sobtop to generate the topology of HEC, and I also modified the aminoacids.rtp, aminoacids.r2b, and atomtypes.atp of force field. Unfortunately, the gmx pdb2gmx failed.