Hi, I need to model linear rigid molecules, CO2. I understood that the virtual site have to be introduced to model CO2 like below way.
[ atomtypes ] ; type mass charge ptype c6 c12 D1 22.004975 0.0000 A 0.0000 0.00000000 D2 22.004975 0.0000 A 0.0000 0.00000000 C_CO 0.0000000 0.5406 V 0.0000 0.00000000 O_CO 0.0000000 -0.2703 V 0.29847 1.10765301 [ moleculetype] . . . etc. However, my question is that I don't know how to give coordinates of dummy particle to the initial coordinate file(i.e., my pdb file) which already has coordinates of C, O, and O but not dummy particle yet. My simulation case is not standard, so pdb2gmx is not working. I have to build each file by hand. Thx.
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