hello, i would like to generate a TFE solvent box for my simulation.I have created a pdb file containing the 1000 TFE molecules in the cubic cell having dimension 40.Now i want to convert it into gro file and call it in the gromacs simulation . can any one help me in generating gro file of TFE.I have "tfe.itp" file. Should I change something in the *.rtp file. I tried using PRODRG but it has limitations of only 300 atoms. I am gettin error like this PRODRG cant model most non carbon -halogen bonds can any one help me in getting gro file for TFE. Thanx in advance
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