I am interested in performing MD simulation for one of the DNA demethylase enzymes using Amber. I have been able to generate both the "mol2" and "frcmod" files for the non-standard residues using Antechamber and parmchk respectively. However, I am finding it difficult to generate parameters for DNA. Please, kindly help me with suggestions on how I can get this done.
Pl see the link for solution of your problem
http://archive.ambermd.org/201004/0272.html
The parameterization procedure is the same with ligand: RESP charges + gaff parameters. If you think gaff is not good enough you can generate bonded parameters and vdW parameters yourself. Of course, it is a bit costly.
For DNA you have to load all the nucleic acid library in leap and then load your DNA structure, save it in pdb or mol2. Then do the antechamber calculation.
For the non-standard DNA residues, you should use the same atome type in your mol2 and frcmod" files, than conventional DNA . If you do like this, tleap program reads directly the deoxyribose and phosphodiester linkage parameters from AMBER nucleic acid libraries. I used this protocol in the past, it works: Article Structural and Dynamical Impact of a Universal Fluorescent N...
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