Index of /mardigras/utilities/mardi2amber

      Name                    Last modified       Size  Description


[DIR] Parent Directory        24-Jan-2001 11:24      -  
[DIR] Examples/               24-Jan-2001 11:22      -  
[TXT] NEW_mardi2amber.f       06-Feb-2001 11:29     9k  


	mardi2amber - version 2.0 - Jan. 2001

mardi2amber-converts mardigras distance bounds for input  to
amber module sander


DESCRIPTION

mardi2amber is an interactive program that  converts  
mardigras distance  bounds for input to the sander module 
of the amber programs. 

The nmr distances with their lower and upper bounds  can be 
obtained from MARDIGRAS, but any file with lower and upper 
bounds can be used as input for this program.
The user has the choice of which columns should be read as
lower and upper bounds input for mardi2amber.

A pdb file is also required as input by mardi2amber.
In fact, mardi2amber reads the atom number that follows the 
ATOM keyword in each line of the pdb file to specify the 
atom in the output file in sander format.
Thus, the position of the atoms in the pdb file must be the 
same when running sander (or the atom pair will be mistaken).
Moreover, atom names in the input pdb file must be consistent 
with atom names used in the input constraint file.

The sander restraint is a flat-bottomed well with  parabolic
sides  initially  and  linear  sides  beyond  the  parabolic
region. The geometric parameters r1, r2, r3, and r4, and the
force  constants  k2 and k3 used to describe the sander restraint 
are defined in the sander  documentation.  


INSTALLATION

To compile the program type the following command at the prompt 
(a fortran compiler is required) :

f77 -o mardi2amber mardi2amber.f

This program was written on a SGI workstation and may not compile
on other platforms.


INPUT

pdbfile:
A pdbfile to provide the correct atom names and atom numbers
required  by sander. The atom names in the pdbfile also need
to be consistent with atom names in the distance  constraint
file. 

constraint file:
An distance constraint file created  by  avgbnds  (or  other
programs  which  writes  out  the  distance  constraints  in
appropriate  format)  using  the  .bnds  (or  .BNDS)   files
obtained from several mardigras runs.
Atom names from mardigras which begin with Q, M or R (mardigras 
pseudoatoms) are described as group atoms by sander.
NOTE: the program recognizes pseudoatoms the way they are 
defined by mardigras (M = methyl , Q = methylene , R = ring protons).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 NEW February 6 2001 :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 CONSTRAINT FILE, ATOM NAMES FORMAT :
	if the format of the constraint file is different, it is 
	easy to adapt the program to the different format, all you
	need to is :
		- change in the source code the value of
		  iat1,ire2,iat2,ire2 that specify the column 
		  positions for atom names and residue numbers :
               		(iat1) name and (ire1) residue # for atom 1
               		(iat2) name and (ire2) residue # for atom 2

                  for example if the constraint file has a format
                  like this :

                  HA1  1 HB1  1   3.6     4.5
                  HA1  2 HB1  2   2.6     5.3
                  HA1  3 HB1  3   3.4     4.2
                   ^   ^  ^   ^
                   1   2  3   4   <--- column #

                  set values to : iat1=1 
				  ire1=2 
				  iat2=3 
				  ire2=4

		  (this is how the program is currently set, so if you 
		   your constraint file looks like the example above, you
		   don't have to do anything)
	
                - compile the program
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Instead, the column position for lower and upper bound is asked 
interactively by the program.


Interactive Input - mardi2amber prompts the user for:

(i) The name of the input distance constraint file.

(ii) Which two columns of the constraint file are the  lower
     and upper bounds?

(iii) The name of the pdbfile.

(iv) The name of the output file to be created for input  to
     sander.

(v) The force constant k2 and k3 for the potential  well  at
    the upper and lower bound. mardi2amber assumes k2 equals k3,
    and ALL RESTRAINTS HAVE THE SAME WEIGHT.

(vi) The width of the parabolic wall.  (The geometric parameters  
     r1, r2, r3, and r4, and the force constants k2 and k3
     are defined in the sander and interface documentation.)

     r1 = lowerbound - width of the parabolic wall (r1 is set  to
     0 if less than zero)
     r2 = lowerbound
     r3 = upperbound
     r4 = upperbound + width of the parabolic wall


BUGS

Restraint weights for  individual  restraints  are  all  the
same.  

The atomic number following the keyword ATOM in each line of
the pdb file is used to identify the atoms in the output file
in sander format.

Atom names in the pdb file must start at column 13 or 14 (if
they start after column 14 they will not be recognized).

No letters are allowed to define the residue number 
(e.g. residue number "10A" won't be read by mardi2amber).


CONTACT

Address questions and problems to:
Marco Tonelli
E-mail: tonelli@picasso.nmr.uscf.edu



Last update - 2/6/01