Dear all, I am having the troubles to obtain the topology file for Cytochrome C. When I used the Gromos96 53a6 force filed in the GROMACS 4.0.7 software package, the topology file is produced, but there is lack of some force field parameters, such as the bonds from Cys 14 and Cys 17 to the porphyrin ring and to hold the ligands (Met 80 and His 18) bound to the heme iron, in this file. When I used the Gromos96 53a6 force filed in the GROMACS 4.5.1 software package, there's a fatal error: Residue 'HEM' not found in residue topology database. I have checked the rtp file, in which there is the "HEME" residue. Who knows how to solve it? Any tip is appreciated, thank you very much!
Hui Sun
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