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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