Instructions for analysing ligand interactions with ZMM

1) Place abcd.pdb in a working directory

2) Inspect abcd.pdb with an editor (notepad in Windows, vi or TextEdit in Mac)  and with PYMOL

            - keep only one monomer (if not interested in dimers or oligomers)

            - take note of the residue number of the ligand (say A_201, A_202)

3) open a terminal at the directory of the pdb

            - Windows, "run cmd", or click "Windows PowerShell" and cd to your directory

            - Mac, - open "Terminal.app" in the utility folder or

                        - open "System Preferences and select Keyboard > Shortcuts> Services

                        - under Files and Folders - click on "New Terminal at Folder"

                        - now you can open terminal at the directory of choice

4) type "zi abcd.pdb  -iw -o"

5) inspect abcd.0.tsk and check for missing atoms - see note A & B below.

6) copy abcd.0.tsk to abcd.kmsr.tsk

7) edit abcd.kmsr.tsk - see notes A & B below

            - remove all "#" in front of all UPPERCASE lines

            - add "PART A_201 A_202"

            - change to "LIMIT 20"

            - change to "LIMIN 200"

8) type "zs abcd.kmsr.tsk"

9) inspect "abcd.kmsr.list"

10) if total energy is positive go back to step 7 and increase the number after LIMIN, e.g. LIMIN 2000

11) You can always stop the stop if you see energy is becoming negative on terminal by deleting "abcd.kmsr.kill_to_stop"

12) if total energy listed in abcd.kmsr.list is negative, check "Receptor interactions"

            - Ligand-receptor total should be negative, if not try to find bad contacts by checking the list of interaction energy below in the same file

            - you can increase the number of LIMIN further to see if the energy would get better.

13) Take note of interactions with large positive or negative energy and inspect the structure (abcd.kmsr.pdb) by pymol

 

 

Note:

A) Example of missing atoms in abcd.0.tsk file

RESIDUE SETTINGS

# NORA

# Residues with atoms not in template. Delete # to MC-minimize

# with sampling these residues and freezing other residues

# RELR  'A___3 '

# RELR  'A_446 '

# RDR   'A_446 '

# Atoms, which are not the template are listed below.

# You may excluded them from model by removing #,

# or you may use key KMSR for multi-step relaxation

# AEXC  ' CG .GL- .A___3 '

# AEXC  '1HG .GL- .A___3 '

...

 

B) Example of updated abcd.kmsr.tsk

RESIDUE SETTINGS

PART A_201 A_202

NORA

# Residues with atoms not in template. Delete # to MC-minimize

# with sampling these residues and freezing other residues

RELR  'A___3 '

RELR  'A_446 '

RDR   'A_446 '

# Atoms, which are not the template are listed below.

# You may excluded them from model by removing #,

# or you may use key KMSR for multi-step relaxation

AEXC  ' CG .GL- .A___3 '

AEXC  '1HG .GL- .A___3 '

...

PARAMETER

  KMSR  1

  KOPT  2

  LIMIT 20

  LIMIN 200

  KPM   1

END