Dear gromacs users, Thank you for your answering my previous questions. Here, I am in trouble again. I continue the simulation of DNA, carbon nanatube and water. I changed the names of atoms in cnt.pdb according to the names in ffamberXX.itp. When I performed the energy minimization, the result I get is :
"Fatal error: Invalid order for directive defaults, file ""ffamber99.itp"", line 4". I checked back ffamber99.itp, the whole file is simple : "#define _FF_AMBER #define _FF_AMBER99 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include "ffamber99nb.itp" #include "ffamber99bon.itp" " Can you give me some suggestions and help me out? Also, I have a question regarding the residue names in amber99. I guess that I may also need to change the residue of CNT(carbon nanotube) according to the residue names used in ffamber99. Do you think that it is necessary? And, how can I do it? Thank you so much! Bo
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