Adventures in Computational Chemistry

Packmol is a software that allows you to generate a single combined PDB file for all the molecules you are considering. It is a free software and can be downloaded from this link: http://www.ime.unicamp.br/~martinez/packmol/ The installation guide is also provided on the page and its really easy to follow. http://www.ime.unicamp.br/~martinez/packmol/ You can also find some examples but I tried on my own. Anyway what you need is an input file which looks like: ------------------ tolerance 2.0 output trial.pdb add_amber_ter filetype pdb structure 2a.pdb   number 1   inside cube 0. 0. 0. 10. end structure structure 2d.pdb   number 1   inside cube 0. 0. 0. 10. end structure --------------------------------- IT includes some information like: how close the molecules considered can be.(tolerance) name of output pdb file "add_amber_ter" adds term "TER" after every molecule thus defining the start and end of every molecule. After mentioning the

Sometimes you totally fail to go ahead with the prepin and frcmod files you have generated from the newly generated PDB file even after you follow the procedure given in previous two posts. And you keep wondering? In such a case you need a more detailed procedure. First take a look at the pdb file. For example: Here is one such pdb file generated from the gabedit that troubled me for some time. --------------- HEADER    PROTEIN COMPND    UNNAMED AUTHOR    GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011 ATOM  1      C   C     1       -2.907  -0.997  -0.385  1.00  300.00          C 0.0000   ATOM  2      N   N     1       -2.060  -0.981  -1.189  1.00  300.00          N 0.0000   ATOM  3      C   C     1       -1.026  -0.973  -2.172  1.00  300.00          C 0.0000   ATOM  4      H   H     1       -0.409  -1.865  -2.044  1.00  300.00          H 0.0000   ATOM  5      H   H     1       -0.409  -0.082  -2.038  1.00  300.00          H 0.0000   ATOM  6      H   H     1      

In earlier post we saw how we create pdb files for the structures we want to consider for multi component molecular dynamics analysis. So now we have say PDB files for four structures - an aldehyde, nitrile, amine and a phenol molecule. Now, In the first step we generate the prepin files for all these molecules by  using: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 Here the molecules are neutral in nature. If you are working with ionic systems you need to add -nc flag in the end followed by charge of the moelcule. So, if the moelcule has +1 charge, the command will be: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc 1 If it is -1, command is: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc -1 If you have followed earlier preocedure properly then your prepin file should be created in no time. You can see some lines of a prepin file as

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

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