[gmx-users] Simulating Protein+Dextran/PEG

Vigneshwar Ramakrishnan vmsrvignesh at gmail.com
Wed Jun 11 05:01:21 CEST 2008

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,

Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of 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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