From: Lv Shouqin (shouqinlv_at_hotmail.com)
Date: Sat Feb 14 2004 - 23:14:38 CST
For help from all!
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!
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