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Structure sampling with Amber

Structure sampling with Amber and

This document described how to setup a parallell molecular dyanamics run using Amber and



  • Amber (7 or higher)
  • Biskit installation
  • 10 computers reachable via ssh without password
  • PDB with protein structure


  1. Check, clean up model, identify disulfide bridges (WhatIf web)
  2. build amber topology (tleap)
  3. run Ensemble simulation (
  4. convert result to Biskit.EnsembleTraj object
  5. fuzzy-cluster the trajectory

Detailed instructions

1. Clean up model (manually)

Create project folder:

mkdir my_topology
cd my_topology

Delete hydrogens from PDB

Go to the whatif web interface:
    - HIS protonation
            Hydrogens / Add protons
            save hadded.pdb to my_topology
    -> note how whatif protonated HIS residues (NE, ND, or both)
    - ASN or GLN flips
            Hydrogen / optimize h_bond network
    -> note, which ASN, GLN have to be flipped (end of result page)


Do not use hadded.pdb for subsequent steps! The whatif atom names are incompatible with Amber.
  • identify S-S bridges (e.g. in VMD)

  • edit original PDB file:

    • rename D-protonated HIS to HID

    • rename E-protonated HIS to HIE

    • rename dual-protonated HIS to HIP

      D-protonated means the H sits on ND; E-protonated (the normal case), it sits on NE; double-protonated means there is a H on both Nitrogen atoms in the ring.

    • rename CYS involved in S-S bond into CYX

    • switch OE and NE of ASN and GLN where suggested by WhatIf

    • remove terminal OT1, OT2 atoms from peptide chains

    • remove terminal P, O1P, O2P from DNA chains

    • remove hetero atoms (except you have prep files for them)

    • remove all hydrogen atoms:

      >>> m = PDBModel('mystructure.pdb')
      >>> m = m.compress( m.maskHeavy() )
      >>> m.writePdb( 'in.pdb' )
    • alternatively you can try to create the correct amber hydrogen names:

      >>> m = PDBModel('mystructure.pdb')
      >>> m.writePdb( 'in.pdb', amber=1 )
Note: the classes used by of biskit/scripts/Mod can probably be adapted to automate most of the above.
2a. Build topology (manually)
>>> cp ../cleaned.pdb ./in.pdb

Select force field

>>> ln -s $AMBERHOME/dat/leap/cmd/leaprc.ff99 ./leaprc

run $AMBERHOME/exe/tleap, in tleap enter:

source leaprc

  ## optional:
  ## load definition and parameters for non-standard residues
m = loadAmberParams your_own.mod
m = loadAmberPrep your_own.prep

a = loadPdb in.pdb

  ## connect SG atoms of S-S bonds
  ## Note: use e.g. 'desc a.9' to check atom content
bond a.9.8  a.38.8
bond a.16.8 a.35.8

  ## add solvent
  ## consider using larger distance buffer and solvateOct
  ## Amber 7 usage:
  ## solvateBox a WATBOX216 10.0
  ## OR Amber 8 usage:
solvateBox a TIP3PBOX 10.0

  ## add counter ions to neutrality (Na+ or Cl-)
addIons a Na+ 0

check a
        -> "Unit is OK."
  ## save topology and initial coordinates
saveAmberParm a top.parm raw.crd

  ## quit tleap

Create PDB file from amber topology and coordinates

>>> ambpdb -p top.parm < raw.crd > raw.pdb
2b. Build topology (automatted)
>>> -i |PDBfile| [-o |out.parm| -fmod |external.mod|
>>>                   -fprep |external.prep| ... ]

This creates out.parm, out.crd, out.pdb, (and leap.log in current folder)

The current version works for Amber 11. Adapt the template in Biskit/data/amber/leap/solvate_box.leap!

3. Prepare folder and run MD

Create result folder

>>> mkdir my_ensemble_MD
>>> cd my_ensemble_MD

Fill folder from standard MD template (in biskit cvs)

>>> -parm ~/my_topology/top.parm \
>>>                     -crd ~/my_topology/raw.crd \
>>>                     -pdb ~/my_topology/raw.pdb \
>>>                     -nb_nodes 2
>>>                     -nodes_eq computer1 \
>>>                     -nodes_prod computer2 computer3 ... \
>>>                     -n_steps 125000
Note: type for help

Run equilibration and wait for it to finish

>>> ssh computer1  ## important! must be on nodes_eq
>>> cd my_ensemble_MD
>>> ./start_eq.csh

Run simulation (can be on any node)

>>> ./start_prod.csh
Note: The complete MD setup is stored in Biskit/data/amber/templates_ensemble_pme. Make a copy, adapt it to your needs and use -template |your_copy|.

The template shell script calling sander is in 2_md_xx/2/start.csh* and may need to be adapted to your LAM version.

Note: The current setup works for Amber 11. Amber 7 required slightly different input files, see Biskit/data/amber/template_pme_ensemble_amber7/!
4. Convert amber result to pickled Biskit.EnsembleTraj object

The result folder contains the coordinates of 10 production MDs in 10 folders: e.g. my_ensemble_MD/2????/3????/sim_protein.crd.gz

The following first step should already be done by the MD script, check whether traj_protein.dat exists

>>> cd my_ensemble_MD/2_md_00/3_md_nvt_1ns

Create Biskit.Trajectory w/o water, w/o hydrogens, with amber residue names translated back to standard names

>>> -i sim_protein.crd \
>>>               -o traj_protein.dat \
>>>               -r ../../0_dry.pdb \
>>>               -b -wat -hyd -rnres

Concat the single member trajectories into one EnsembleTraj object

>>> cd my_ensemble_MD
>>> -i 2*/3*/traj_protein.dat \
>>>                  -o traj_ens.dat  \
>>>                  -pdbCode MD1
Comment: Consider using option -step or -s -e to get a smaller trajectory.
5. Clustering of trajectory (select 10 snapshots)
>>> mkdir my_ensemble_MD/clustered
>>> cd clustered

Select 10 snapshots, by CA clustering of every 5th frame

>>> -i ../traj_ens.dat \
>>>                 -n 10 -a CA \
>>>                 -step 5 > cluster.log
Comment: This creates n pickled Biskit.PDBModel instances and a pickled dictionary that contains all of them indexed by cluster number. The dictionary is the input to the Biskit docking routines.

If you need PDB files...

>>> -i *model