Adventures in Computational Chemistry

Returning to xleap again. The box I require this time has little tricky requirements. 1) The box should satisfy the molarity ratio for the solute: solvent. 2) Should be big enough that QMMM calculations can be carried out easily 3) combine sets of molecule-pairs which are interconvertible following a proton transfer. I have a pair of molecules say p(H)--i which can be converted to another set called P--I(H) following a proton transfer from p to i.So, p(H)--i <---> P-I(H) To fulfill condition (1), I initially created one molar box for p(H)--i called "PIN" and other box for P--I(H) called "PII" For condition (2) and (3), I created a bigger box with 7 PIN and 1 PII boxes. The idea is: after proton transfer from I to P, during the QMMM calculation, P--I(H) pair coming from "PII" should convert to p(H)--i pair like other pairs from "PIN" and the whole box should become homogeneous with 8 p(H)--i pairs. We begin with: PIN with ...

GNUPLOT can be used to generate histograms. The script below allows one to plot variations in angle from 0° to 180°. Each histogram box width correspond to 3° (covered here under bw option). To execute this script; type this in the terminal: gnuplot histogram.p You should be in the folder where below script is saved in a file name "histogram.p" and a dat file (here, it is N---H-O.dat) should be present. histogram.p ------------------ set term gif set output "angle_N---H-O.gif" set xrange [0.0:180.0] set boxwidth 2.0 absolute set style fill solid 1.0 border -1 set xtics 10 set title "molecule 3.0A Angle N---H-O" set ylabel "occurance" set xlabel "angle" bw = 3   # substitute what you want bin(x,width)=width*floor(x/width) plot 'N---H-O.dat' using (bin($2,bw)):(1.0) smooth freq with boxes ------------------ The dat file is an input file with data in the format: 0    23.680344 1    73.766251 2    67.4...

Now that we have the lib file with the information for all the molecules we need to include and also the corresponding combined pdb file, creating prmtop and inpcrd files should not be a difficult task. So, to begin with we have a lib file name: molecule.lib a pdb file for 4 molecules name: four.pdb The  task is to generate a prmtop and inpcrd file. Initiate xleap using: $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99 In xleap window > source leaprc.gaff # load the lib file by: > loadoff molecule.lib I am not sure but some times it helps to also load the frcmod files we created for the four molecules the information of which is stored in the lib file. > loadamberparams aldehyde.frcmod # Load the pdb file: > P=loadpdb four.pdb You should see some thing like this in the xleap window now: ------------------- > P=loadpdb four.pdb Loading PDB file: ./four.pdb Warning: name change in pdb file residue 1 ;  this residue i...

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 ...

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 fil...

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...