Dear All, I am a newbie to GROMACS and to MD simulations. I want to simulate and study protein in the presence of Dextran or PEG. 1. From literature and internet searches, I understand that PEG topology file can be generated using the PRODRG server and hence protein+PEG simulations should be possible. But what I am worried is that, the GROMACS forcefields are united atom models. So will I then not be able to study hydrogen bonding in my system? 2. For Dextran, I understand from literature that CHARMM forcefield can be used. I also understand that there are perl scripts to convert the charmm input files into gromacs compatible versions. But can anyone tell me if the perl script available from the GROMACS-user contribution section can handle Dextran? It says that it accurately handles Lipids and silicates but there is no comment about dextran or carbohydrates.
I will be grateful for any suggestions and directions. Thank you, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" "The rewards of sincere resolves are highs money can never buy!"
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