[gmx-users] Simulating Protein+Dextran/PEG

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 11 12:07:46 CEST 2008

Vigneshwar Ramakrishnan wrote:
> 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?

Polar groups in UA force fields represent hydrogen atoms explicitly. 

Be aware that the "GROMACS forcefield" is deprecated and should not be 
used.  The PRODRG beta site will give parameters compatible with 
Gromos96 43a1, but the charges are often unsatisfactory and require 


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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