Hi all,
I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now is that after energy minimization, the protein and water (originally in the protein cavity) were found in completely different coordinate space. Using "pbc box" in VMD, I found that the water was found roughly at the original space but not the protein. I have tried (all turned out futile) 1) EM with and without pbc 2) position restraint the protein backbone and water Would someone be able to help me on this? I know I must have done something silly here. Thank you. Huiwen << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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