Hello gromacs users, I have asked this question before but perhaps I was not clear enough. I noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure has some side chains located very close to each other then after energy minimisation they become distorted (for example, Phe ring is not flat, and for Leu some hydrogen atoms move away from the rest of the side chain).I realize that these problems are probably due very close packing of the sidechains in the initial structure. But I hope to keep the close contacts in the initial structure and obtain correct stereochemistry of the molecule after the minimisation. Is this possible? Sorry for bothering you again and thank you in advance for your help,Abdullah Ahmed
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