Working with a multicomponent system

I have a system with four molecules and the initial challange is to generate a combined PDB file for the four molecules together which is compatible with the AMBER software.
Apparently it is a simple problem. But here it is a problem because pdb version of molecules generated using different build up softwares find compatibility issue with Amber.
Also I found very rare examples where people are trying to study multicomponent system using Amber. In other words even the Amber mailing list (http://archive.ambermd.org/) was not very helpful in solving the problem.
I tried many different possibilities. I used different tutorials for Amber, but none of them were direct solutions.
I finally created my own procedure understanding these tutorials and combining them together.
In coming few I will try to explain how you can generate amber compatible PDB file for multi component system

Comments

Material Studio - selective molecule movement

So, working with Material Studio is awesome. You get to handle bigger, complicated and even unimaginable system. But I am facing problems in very minute functioning. I recently faced two problems, but managed to resolve on my own. Somehow, tutorials doesn't help in resolving them and you end up doing some exercise on your own to get the solution. Among these, the problem of bringing two molecular structures in one window and then adjusting one molecule by moving it around, while other structure remains untouched, as it is. Actually, this should not be a problem to do. There is a simple way of doing this. Select the molecule to be moved and then there is a symbol (button) to select, which allows you to selectively move that molecule only. This is the same way it can be done in Material studio too. But among all the dozens of symbols, the new person handling MS, kind of gets lost. So, what he does is check the tutorials, for any help. But the tutorials don't talk about suc...

Generating a structure PDB file using Gabedit

If Gabedit is installed and functioning on your system, type gabedit in terminal. Gabedit will open and you can find an option "Geometry" in the tool bar. Select "Geometry"--> "Draw" After some trials and playing you will finally learn how to generate a structure. Once your structure is ready, you need to set the atom types and charges. For this click on "M" button in the top left of the "Draw Geometry" window and select options as: M-->"Set"--> "Atom Type & charge using PDB template" Here if you use "Atom Types using connection types", it helps. You can check if the atom type and charge has been set according to the amber requirements by an indirect method. Try to run a quick MM calculation. Run MM calculations by clicking: "M"-->Molecular Mechanics-->optimization It may sometimes end up with a pop up window that suggests that either atom type or charge is not...

Conditions to use different Schrodinger Equation forms

Every molecular system has an energy associated with it. This energy might show a shift depending on the surrounding environment or internal variations. Magnetic dipoles present in a molecular system in the form of electrons and the nuclei is one such reason for the energy shift. But the effect of these magnetic dipoles on the energy shifts will be much less which can be accounted by considering perturbation theory. Chemical binding energies on the other hand are responsible for the major shifts in energy of a molecular system. Thus the focus is shifted towards the valence electrons responsible for most of the chemical activity of a molecule. The valence electrons are separated from the core electrons. The core electrons are treated approximately. This reduces the efforts of considering the relativistic effects affecting the core electrons, and thus can now be ignored. What are relativistic effect? It has been nicely explained by Ermler and Pitzer in the introduction of th...

Adventures in Computational Chemistry

Search This Blog