<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><br></span></div><br>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div id="yiv1914220862"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents".</div><div>Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp.</div><div>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,</div><div>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.<br></div><div><br></div><div>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.</div><div>Is there any other file for co-solvent interactions I need to
change?</div><div><br></div><div>Thanks,</div><div><br></div><div>Yao<br></div></div></div></div><br><br> </div> </div> </div></body></html>