<div>Dear All, </div>
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<div>I am a newbie to GROMACS and to MD simulations. </div>
<div>I want to simulate and study protein in the presence of Dextran or PEG. </div>
<div>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? </div>
<div>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. </div>
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<div>I will be grateful for any suggestions and directions. </div>
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<div>Thank you, </div>
<div>Sincerely, </div>
<div>Vignesh</div>
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<div><br clear="all"><br>-- <br>R.Vigneshwar<br>Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br>
<br>"The rewards of sincere resolves are highs money can never buy!" </div>