Adventures in Computational Chemistry

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...

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...