Adventures in Computational Chemistry

I needed to delete all the lines in a set of files except for for the first forty. Since the number of files was big, I used this script in python to do the job: -------------------------------- !/usr/bin/python #script to read files and delete lines import os listing=os.listdir(" /home/kjoshi/Documents/PY/useful/file_edit ") for infile in listing:  print infile  if infile == "files_line_delete.py":    print "This is NOT a good file"  else:   fi=open(infile).readlines()   fo=open(infile +'_output','w')   del fi[40: ]   fo.writelines(fi) --------------------------------- Task is simple. Keep all the files needed to be edited in one folder along with this script. Substitute the path shown in bold with proper path of your folder. Using command $python files_line_delete.py you get output files with each file having first forty lines.

The task was to create a set of folders say 1,2,3,4 and in each of these four folders create four sub folders. Thus 16 folders were to be created and in each of these 16 folders a common set of files were to be copied. I used c shell scripting to do the job. I needed two lists. One list for primary folders list1: 1 2 3 4 and another list for the subfolders. list2: 5 6 7 8 It worked as: ------------------- bash-3.2$ csh r410comp2% r410comp2%foreach f (`cat ../list1`) foreach? echo $f foreach? mkdir "$f" foreach? cd "$f" foreach? foreach g (`cat ../../list2`) foreach? echo $g foreach? mkdir "$f"_"$g" foreach? cd "$f"_"$g" foreach? cp /home/kjoshi/W/work/complex/2_ion/umbrella/6/6_75/u_6_75.in . foreach? cp /home/kjoshi/W/work/complex/2_ion/umbrella/6/6_75/amber11_intel_ref_md . foreach?cp /home/kjoshi/W/work/complex/2_ion/umbrella/6/6_75/2_ion.inpcrd . foreach?cp /home/kjoshi/W/work/complex/2_io...

This script allows one to exchange two columns in a file.And it do so for all the files in a directory. The python script is : ---------------------------- #script to read and execute column exchange for all files in the directory import os listing=os.listdir(" /home/K/Documents/PY/column_exchange ") for infile in listing:  print infile  if infile !="column_interchange_script.py":   fi=open(infile).readlines()   fo=open(infile +'_output','w')   space="   "   for line in fi:    first,second=line.split()    fo.write('%s%s%s\n'%(second,space,first))  else:    print "This is not interesting file"     ----------------------------------------------------    Some expert might simplify it a lot more, but for new python user like me, this is a big leap. So, how does it work: Create a directory where in all the files for which column exchange need to be done are stored. Kee...

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...