I am doing my Ph.D. in Materials Science and am completely new to Molecular Dynamics Simulation and Linux. I am using Manjaro Linux 20.1 and have Gromacs 2020.4, VMD 1.9.3, packmol 20.0.10, AmberTools 20.9 installed. I have been following the tutorials by Prof. Justin Lemkul, but they do not address building a polymer from a monomer file. I want to build the polymer PNIPAAm from the monomer NIPAM. I have obtained the NIPAM PDB from here: https://atb.uq.edu.au/molecule.py?molid=363683
I have used the Polymer Modeller Tool on https://nanohub.org/tools/polymod/
I am getting a wrapped and unwrapped structure, and I am not really sure if the polymerization occurred correctly.
When I use the resulting PDB files in Gromacs by using the pdb2gmx command, an error comes saying that the residue type is now known.
I am also attaching all the PDB files.
So at this point, I am completely clueless about a lot of things and would like to know if there exist any tutorials regarding how to build an initial configuration file or building our own PDB files, how to create our own mdp files, etc.
A complete course would also be helpful.
Dear Phani
1- you couldn't build a polymer with monomer pdb file with GROMACS, I suggest you use Material studio or Guass view for constructing your molecules.
2- Pdb2gmx is a command that gives topology for proteins and DNA. This command is not applicable to other molecules.
For other molecules, you could some servers that build topologies such as ATB and Swiss param
https://atb.uq.edu.au/index.py
http://www.swissparam.ch/
http://zarbi.chem.yale.edu/ligpargen/
Hope it helps
Hello Phani! Sure you can get a topology for any molecule using pdb2gmx command of Gromacs. If you get an error message which says that your residue was not found in the database it means that in your pdb-file the name of residue is non-existent in rtp-residues and that you have to add that rtp-residue to the desired force field by yourself manually. You have to create the name of that residue and name every single atom with its unique name. If you do not know what charges you would have then you shall perform quantum chemical calculations on a relatively number of polymer conformations in order to derive charges. When you have charges you can add you residue to rtp-database. I suggest you also to check how rtp-files look like in the desired force field and then you can make your own. When the residue will be added you will get your itp and top files. Additionaly, I can say that it might happen that you might need parameters for angles and dihedrals. You shall check what exists in the force field for your polymer.
Take a look at the “Polymer Builder” of CHARMM-GUI:
http://www.charmm-gui.org/?doc=input/polymer
It’s very convenient. Also there is a video demo on Youtube here: https://youtu.be/ICnnEfEp2aQ
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