[gmx-users] Modified peptides

sun sun.iba2 at gmail.com
Sat Apr 2 08:11:19 CEST 2016

Hello Gromacs Users
I have already posted this query but in the absence of any suggestion, I am posting it again. I hope someone will help me. I am going to do protein-peptide MD using Justin's protein-ligand tutorial (ff gromos43A1, GROMACS version 5.0). My ligand is a pentameric modified peptide. In the tutorial, I studied that Gromos96 parameters are obtained from PRODRG server but due to less uniformity in charges, it is not 100% reliable. Its allright, Charges can be corrected from the paper that is cited in tutorial. But, I have also read that for modified peptides or sequences, we can make changes in force fields manually. So, my query is, which option would be more suitable for my peptide? Is it OK to obatin co-ordinates for modified amino acid from PRODRG? 

With Regards

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