Ambertools16

                                         Installation:

(1) Download AmberTools16.tar.bz2 from http://ambermd.org/AmberTools16-get.html

(2) bunzip2 AmberTools16.tar.bz2

(3) tar xvf AmberTools16.tar

(4) cd amber16

(5)  export AMBERHOME=/home/myname/amber16 # (for bash, zsh, ksh, etc.)
      setenv AMBERHOME /home/myname/amber16 # (for csh, tcsh)
      (if needed, you may need to install csh: sudo apt-get install csh)

(6) You may need to install flex, bison and some compilers and other libraries
      (use synaptic package manager or apt-get)

(7) ./configure gnu  (if needed, switch over to csh)

(8)  source /home/myname/amber16/amber.sh # for bash, zsh, ksh, etc.
      source /home/myname/amber16/amber.csh # for csh, tcsh

(9) make install

(10) make test

Useful tips:

(1) pdb4amber -i input.pdb -o output.pdb [options]
(2) $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.DNA.bsc1 -f $AMBERHOME/dat/leap/cmd/leaprc.water.tip3p 
(3) In xleap window: 
      (a) to load a pdb file
            bdi=loadpdb "output.pdb"
      (b) to see and edit the structure
            edit bdi
      (c) to see the list of structures loaded
            list
      (e) to save prmtop and inpcrd:
            saveamberparm bdi bdi.prmtop bdi.inpcrd 

Tutorial: 
(http://ambermd.org/tutorials/advanced/tutorial2/section1.htm)

system:  N-methylacetamide (NMA) in a periodic box of TIP3P water
input PDB: NMA_skeleton.pdb
content of NMA_skeleton.pdb is as follows (missing atoms will be guessed):

ATOM     1   C   ACE     1       0.000   0.000   0.000
ATOM     2   N   NME     2       3.000   1.000  -1.000
TER

step1:  $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB

step2: nma=loadpdb "NMA_skeleton.pdb"

step3:  edit nma (to energy minimize)

step4: Edit->Relax

step 5:  Unit->Close

step6:  source leaprc.water.tip3 (load solvent parameters)

step7: to add water box:
solvatebox nma TIP3PBOX 15 (here, buffer=15 A, which means that the distance between any atom of NMA and the edge of the box is at least 15 A)
step8:
saveamberparm nma nma.prmtop nma.inpcrd

Our B-DNA model:
step1: remove hydrogens from DNA
step2: add 'TER' after DNAA and DNAB
step3: change residue name of water from TIP3 to TP3
step4: change OH2 of water to O
step5:$AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB -f $AMBERHOME/dat/leap/cmd/leaprc.DNA.bsc1
step6:  In xleap window: source leaprc.water.tip3p
step7: bdna=loadpdb "l_noh.pdb"
step8: saveamberparm bdna bdna.prmtop bdna.inpcrd
step9: savepdb bdna bdna_amber.pdb

For parmbsc1:
 refer: http://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download#instructions

source $AMBERHOME/dat/leap/cmd/leaprc.ff14SB

loadoff parmBSC1.lib
 loadamberparams parmBSC1.frcmod

To visualize AMBER trajectory using VMD:
----------------------------------------

step1: File -> New Molecule -> select file.prmtop (if required, specify the file type as "AMBER7 Parm")
step2: select "Load Data Into Molecule" and load the trajectory file (file.dcd). Here, you need to specify the input dcd file type as "CHARMM,NAMD,XPLOR DCD Trajectory".

To set the topology and parameters for a new residue/fragment:
--------------------------------------------------------------
read: http://ambermd.org/tutorials/advanced/tutorial1/section3.htm

To model proteins:
------------------
Note1: There are three types of histidine (HIS in normal pdb files) residues in AMBER:
      

HID: Histidine with hydrogen on the delta nitrogen (HSD in CHARMM)
HIE: Histidine with hydrogen on the epsilon nitrogen (HSE in CHARMM)
HIP: Histidine with hydrogens on both nitrogens; this is positively charged.
It is up to the user to inspect the environment of each histidine and identify the type that is appropriate.

Note2: Change ILE CD to CD1
Note3: Change CGLY OT1 to O;
             Change CGLY OT2 to OXT
Note4:  Remove all hydrogens of the protein from the pdb file

STEP1:  $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
STEP2: In xleap window: loadamberparams frcmod.ff99SBnmr (You may need to download frcmod.ff99SBnmr from Bruschweiler's website and copy it to $AMBERHOME/dat/leap/parm folder).
STEP3: source leaprc.water.tip3p
STEP4: ubq=loadpdb "ionized_nohyd.pdb"
STEP5: saveamberparm ubq ubq.prmtop ubq.inpcrd
STEP6: savepdb ubq ubq_amber.pdb

AMBER parameters for simple molecules and cofactors:
------------------------------------------------------------------------------------------
http://research.bmh.manchester.ac.uk/bryce/amber
http://upjv.q4md-forcefieldtools.org/REDDB/projects/F-90/

How to cite Ambertools16:

D.A. Case, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, W.M. Botello-Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.

voro++/zeo++

zeo++
---------

(1) The radii of atoms are tabulated in networkinfo.cc. If needed, you could define new atom types and assign atomic radii of your choice here.

(2) Box/unit cell vectors: a is aligned with the x-axis and b is in the xy-plane.

(3) The format of the output of the stochastic ray tracing option:
      x y z dx dy dz magnitude
      Here, magnitude = sqrt(dx*dx + dy*dy + dz*dz) and, for a given ray shooted into the free volume region, it provides a measure of the norm of that ray . I think, x y z are the coordinates of the starting point of the ray (not sure!). I think, the way to understand the output is as follows: A given ray starts from (x,y,z) and extends by dx, dy, and dz units along the x-, y-, and z-axes, respectively.

(4) Pore diameters:
     First value: D_i (Diameter of the largest included sphere).
     The largest included sphere points to the location of the largest cavity in the system and D_i measures the size of this cavity.

     Second value: D_f (Diameter of the largest free sphere).
      The largest free sphere corresponds to the largest spherical probe that can diffuse through the structure and D_f measures a minimum restricting aperture on a diffusion path.

     Third value: D_if (Diameter of the largest included sphere along free sphere path).
     D_if is a measure of the size of the largest cavity along free sphere path/diffusion path.

(5) The distance grid option is possible. The energy grid option is not available.
      Distance grid:
      A grid representation of the system is used.  Each grid point is assigned a distance to the surface of the nearest atom. The radius of the largest included sphere is then equal to the maximum value over all grid points. The clusters of neighboring grid points with the assigned distance values above a threshold corresponding to the probe radius are identified and connected to calculate the largest free sphere.

The energy grid option, in principle, can be used to estimate the net activation energy for diffusion of a probe through the system.

 (6) Voronoi netowrk:
        - Voro++ is used
        - voronoi cell associated with each atom is computed individually
        - the collection of edges and vertices/nodes of individual voronoi cell is stored
        - for each edge and vertix of the voronoi cell of an atom, the minimum distance to the atom is also stored. This distance is the distance to the surface of the central atom if its radius is specified (otherwise it is the distance to the center of the atom).

(7) To visualize the network:
      -  cd zeovis
      -  open ZeoVis.tcl and change the path to the network executable. 
      -  vmd -e ZeoVis.tcl
      -  You will be asked to provide the filename of your input file (i.e., the structure file). After providing the input filename, nothing will be displayed on the graphical window of vmd. Do not worry!
      - to show all atoms: show atom all
      - to show all nodes: show node all
      - to show the voronoi cell of an given atom (say, with index 4): show vorcel 4
      - to undo : undo
      - to show unit cell : show unitcell