I am trying to do the molecular dynamics simulation of a protein complex using the program NAMD. Unfortunately, because of the including of small suger part and a abnormal sulfated amino acid in the complex, and the lacking of the topology and parameter files of the suger part and the abnormal amono acid in CHARMM force field, the simulations can’t go on smoothly. Incidentally, I found the force field files “toph3.cho, param3.cho” for the suger part, and “top.so4, param.so4” for SO42- in XPLOR, and especially the remarks of “toph3.cho, param3.cho” are that they can be used with CHARMM19 protein parameters, then I take it for granted that they can be used with CHARMM22 protein parameters too.
So, ignore of the emphasizing of “toph3.cho, param3.cho” for “structure refinement”, I want to do the molecular dynamics simulation of my protein complex with cooperated force field files, i.e. CHARMM22 for the protein part of the complex, “toph3.cho, param2.cho” for the suger part of the complex, and the combination of CHARMM22 and “top.so4, param.so4” for the abnormal amino acid.
Now, the simulations can go. But, whether is the cooperation feasible or not? How can I prove the feasibility? If not, How can I solve this problem better? Did you meet this kind of difficulty in your work, and would you please give your judgement in your convenience? Thank you very much!
Last edited by alex; 03/11/04 11:02 PM.