Hi All, I am running simulation of a system containing Coarse Grained 1SU4 (Minimized structure) and Coarse Grained DPPC lipid. I used the INFLATEGRO script to inflate the lipid and removed the overlapping lipids with proteins and then running the energy minimization.
grommp says there are mismatching of atoms in system.top file (which consists of DPPC, Protein and W) and inflated_bilayer.gro (Which Inflategro script developed). I don't know why this is happening and why the atoms are not matching. Also, is there any problem with the atom2cg.awk script which MARTINI guys provided or they have any other script which converts the atomic structure of protein to CG protein so that at the time of simulation the atoms match. I am using the grompp command something like this. grompp -f em.mdp -c inflated_bilayer.gro -p system.top -maxwarn 10 grompp says: atom name 1 in system.top and inflated_bilayer.gro does not match (NC3-BCQd) and it keeps on going until 2116 atoms. I dnt know how to fix this. Reply will be appreciable. Thanks, Sunny
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