Charmm-gui MD setup for namd

MUTATE:
1. Pymol - Wizard/Mutate
2. Check/fix new atom names

NEW LIGAND:
1. Create .mol2 file with all hydrogens 
2. Create PDB file with exact same names
3. Combine target and ligand PDB files in the desired starting conformation
4. If there is a previous ligand-target complex, the new ligand can be superimposed on the old one by the Pymol pair_fit command:

pair_fit M1////a11, M2////a21, M1////a12, M2////a22, M1////A13, M2////a23

where M1 and M2 are the two molecule names, and atoms a1i and a2i are the i-th pair of atoms to be matched on molecules M1 and M2, resp.

GENERATE INPUT:
1. Select Input Generator/Quick MS simulator on the Charmm-gui website (http://www.charmm-gui.org)
2. Upload target-ligand complex PDB file 
3. Upload, if any, the .mol2 file(s) for parameter generation
4. Upload, if any, the already existing .prm and .rtf files  
5. Download the charmm-gui.tgz file

SETUP MD run with NAMD:
1. Unzip charmm-gui.tgz, untar charmm-gui.tar
2. Rename directory charmm-gui to the system name, say S
3. Copy all files from /sc/hydra/projects/~mezeim01b/MD_setup to S (use cp -r )
4. cd S/namd
5. source ../namd.fix
6. If there are ligands then for each ligand lig:  cp ../lig/*.prm toppar (copy all .prm files needed for the run to S/namd/toppar)
7. Edit step4.sh to have the right account name, que name and wallclock time
8. Run step4.sh - this performs the equilibration step set up by Charmm-gui
9. When step4.sh completed, copy the coor, vel and xsc files one level up:
    cp step4_equilibration.coor ../prod.0.coor
    cp step4_equilibration.vel ../prod.0.vel
    cp step4_equilibration.xsc ../prod.0.xsc
10. cd .. (back to directory S)
11. mkdir EQ (create directory where 1ns runs will be saved)
12. Edit prod.in:
12.1. If there are ligands then make sure there are calls for lig.prm for each ligand ligand
12.2. If there are no ligands then make sure the calls for lig.prm are commented out
12.3. Change (at the top) .coordinates        step4_equilibration.pdb. to 
     .coordinates        step3_pbcsetup_rotated.pdb
when octahedral periodic box was used or to
     .coordinates        step3_pbcsetup.pdb
when rectangular periodic box was used.
12.4. Adust (if needed) dcdfreq from 1000 to larger (to save fewer frames)
13. Update the que name, account name, # of CPUs, wallclock time limit, and job names in sub_prod.sh (for regular processors) or in gpurun.sh (for runs using GPUs).
14. Update the loop information selecting the job numbers in sub_prod.sh or gpurun.sh
15. Run sub_prod.sh or gpurun.sh