I want simulation cytochrome C with Gromacs package and CHARMM force field , I am using CHARMM GUI for produce .itp and .top file for cytochrome C but output file by CHARMM GUI two amino acids methionine and histidine not bonded with Fe of HEME group cytochrome.
please, help me for simulation cytochrome C.
Dear Stéphane Abel
thanks for your answer
at first, I using GROMOS 43a1 for cytochrome that using others paper worked on this protein but I see this force field not added all hydrogen for structure then I using Charmm27 with pdb2gmx but I have error missing hydrogen and I build block HEME for all hydrogen HEME group in aminoacids.hdb file in Charmm.ff folder but I have missing error again.
finally, I read in gmx mailing list @Justin Lemkul suggested using Charmm GUI.
Also I see charmm27.ff folder in Gromacs package . it has all parameter for Heme group and There is in specbond.dat for MET and HIS but pdb2gmx does not work for cyt c.
I do not Know about BTW.
Hello Stéphane Abel
thanks
I using PDB file suggested you but redox state (PDB id:2frc). I changed the names of Hs and HEC similar to chamm27 force field but for HEME group names of Hs exactly similar to rtp file but I have feta error :
Atom HHA in residue HEME 0 was not found in rtp entry HEME with 73 atoms while sorting atoms.