BILBOMD

BILBOMD - rigid body modeling

and Minimal Ensemble Search

Written by: Michal Hammel , Martin Pelikan & Dina Schneidman

Reference: Pelikan, M., Hura, G.L., and Hammel, M. (2009). Structure and Flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys. 2009 Jun;28(2):174-89.

download : Pelikan2009.pdf

Hardware platforms: in the moment on our LINUX - cluster only

ask MH for acces ( mhammel@lbl.gov )

Short user instructions

The program BILBOMD allows determination of three-dimensional domain structure of proteins based on conformational sampling using molecular dynamics (MD) approach.

MD is widely used for exploring conformational space. A common strategy is to perform the simulation at very high temperature (~1500K), the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. Different conformations of the protein are produced at regular intervals along the MD-trajectory. The produced conformations are validate by subsequent calculations of the theoretical SAXS profiles. The program CHARMM is used for MD simulation. The initial atomic models are taken as the starting point of the simulations. In all cases, only the atoms of the linkers rigid domains and loops are allowed to move, while the domains are treated as rigid bodies, with no internal motion. All conformational sampling are performed with the following protocol.

1. Transforming your initial PDB structure to the CHARMM compatible format.

2. The system is subjected to energy Minimization (MINIMIZED)

3. Heating up linkers to 1500K keeping the protein atoms fixed. (HEAT UP)

4. During MD simulation each registered conformation are compared to the experimental data using the program FOXS

6. Multiconformational model for flexible structures are explored using MES.

!!!!!!!!!!!!!! Do not used capital letters in the directory or files name

> ssh username@bl1231.als.lbl.gov # ask MH for access

> ssh crush

> cd # to your directory where the initial structure (segments.pdb) and experimental data (file.dat) are located.

Starting

sibyls@crush:eap/test 75% bilbomd ◄┘

*********************************************************
****************** BILBOMD version 1.5 ******************
*********************************************************
****writen by Michal, Martin & Dina release 11/2009 ***********
*****should help to everybody who want to used **********
***********MD conformational sampling and MES ***********
************** rigid body modeling **********************
*********************************************************
*********************************************************
*********************************************************

Do you want transfer pdb to charmm? <N>

Y ◄┘

# 1. BILBOMD need to make own *.psf *crd files.

If you have protein complex or oligomer each separate peptide will be separate segment. Please input each segments as individual PDB. BILBOMD take only ATOMs and rename each segment starting by 1.

Do you want minimized? <N>
Y ◄┘

# 2. BILBOMD cleans up the sterical clashes and disconnected loops in initial structure.

Do you want heat up? <N>

Y ◄┘

# 3. BILBOMD heat up the minimized structure to 1500K

Do you want conformational sampling + MES? <N>

Y ◄┘

# 4. BILBOMD start conformational sampling. You will need to respond few question about how long MD needs to be (one run/ one Rg is eq. to 200 conformations). You may run default.

Do you want calculate SAXS from existing DCD files ONLY? <N>
Y ◄┘

# If you want to validate already existing conformations ( stored in *dcd files) with a another experimental data you can run only this step.

ENTERING SEGMENTs

Numbers of segments ? (segment should be smaller then 1000 residues)
1 ◄┘

# If your initial structure have more then one peptide chain input them as separate segments (separate PDBs). Your initial structure will be clean up from REMARKS, HETATOM , change MSE to MET, change dual occupancy residues and renumbered segments (single peptide) starting by no.1.

Enter the output file name ?
filename◄┘

#Input root filename. Do not used capital letters. Charmm do no like it. In this moment Charmm will build up own
<filename>.pdb , <filename>.crd AND <filename>.psf

The residues in the initial structure may be renumbered, please check the files for later rigid domains definition.

ENTERING CONSTRAIN

Do you want make a new const.inp (definition of rigid domains)? <N>
Y ◄┘

const.inp file is the file where the rigid domains are defined.
If you already have const.inp from previous BILBOMD run you may editing this file and change start/end residues manually.

example const.inp

Numbers of rigid domains? #Number of rigid domain including fixed domain.
2 ◄┘

Fixed domain - segment ID?
1 #segment for fixed domain
begin ? #Residues range
113
end ?
207
More residues in the fixed domain - segment ID? ◄┘

1. moving domain - segment ID ? #segment for first domain which will be flexible
1 #Residues range
begin ?
1
end ?
98
More residues in 1. moving domain - segment ID ? ◄┘

ENTERING MD-run

Enter the DAT file
*****.dat ◄┘

example for file.dat

qmax ? <0.3> ◄┘ # Define qmax , default value - 0.3Å-1.

How many runs (1 - 10 )? # 1 run per 1 Rg is eq. to 200 conformations
3 ◄┘

Rg min? # Define in which Rg range you want screen the conformations
40 ◄┘

Rg max ?
50 ◄┘

Steps between Rg min and Rg max?
2 ◄┘

BILBOMD will start

OUTPUT

foxs.out & foxs_parameters.out > validation of all conformations ( filename ,χ²)

meslist.pdb & meslistc.pdb > MES model in pdb format

mes.fit & mesc.fit > MES fit to the experimental data

meslist.sta meslistc.sta > model validation molecule/ RMSD/ RG /Dmax

DCD to PDB

To see your specific conformations (best fit, worse fit etc...) used dcd2pdb command

Usage: dcd2pdb file RG run Start End