I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, .... even when I #include its .itp and change #mols in my new topology.
I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? Thanks, Yao
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