Q.862 - How can I generate XPLOR topology/parameter files for XXX ?

With XPLO2D:

Robert Scavetta asked the following question:

 > We have crystals that have been formed with ammonium sulfate, and our
 > maps indicate that there is sulfate present in the crystal.
 > We were wondering if anyone has parameter, topology, and scattering
 > files for sulfate ?

I assume you mean for X-PLOR (if so, scattering files are not necessary, since the form factors for O and S are in all example input files).

For O users, generating topology and parameter files is simple:

• get pub/gerard/omac/hetero.pdb from the O ftp server
• check if there is a structure with SO4 in it; you will find:

 COMPND SULPHATE DIANION
 REMARK Extracted from PDB file 1p12.pdb
 REMARK Formula O4 S1
 REMARK Nr of non-hydrogen atoms 5
 REMARK Residue type SO4
 REMARK Residue name 611
 REMARK   2 RESOLUTION. 1.90 ANGSTROMS.                                  1P12  39
 HETATM    1  S   SO4   611       0.027   0.048   0.045  1.00 20.00      1P12
 HETATM    2  O1  SO4   611       0.586  -0.075   1.420  1.00 20.00      1P12
 HETATM    3  O2  SO4   611      -1.090   1.027   0.058  1.00 20.00      1P12
 HETATM    4  O3  SO4   611       0.954   0.337  -1.112  1.00 20.00      1P12
 HETATM    5  O4  SO4   611      -0.475  -1.336  -0.409  1.00 20.00      1P12

• paste this into a new PDB file, called so4.pdb (for instance)
• get XPLO2D from pub/gerard/xutil from the O ftp server
• run XPLO2D; select option AUTO and answer some simple questions
• this will give you (among other things), two files, one with the topology and one with the parameters. These files sometimes need editing (e.g., masses, charges, donors, dihedrals). You get two more output files: an X-PLOR input file to energy-minimise the "structure" and a "clean" PDB file which can go straight into X-PLOR.
• the topology file looks as follows:

   Remarks so4.top
   Remarks Created by XPLO2D V. 940816/1.2.1 at Mon Jan 16 22:43:18 1995 for user gerard
   Remarks Auto-generated by XPLO2D from file so4.pdb
   Remarks You *MUST* check/edit MASSes and CHARges !!!

   Remarks Check DONOrs and ACCEptors
   Remarks Verify IMPRopers yourself
   Remarks UNcomment any DIHEdrals you want to use

   set echo=false end

   { edit masses yourself !!! }
    MASS SX1  32.06000 ! ADD 1.008 for each H
    MASS OX2  15.99940 ! ADD 1.008 for each H

   autogenerate angles=true end

   RESIdue SO4

   GROUp
     ATOM  S    TYPE SX1   CHARge  0.0  END
     ATOM  O1   TYPE OX2   CHARge  0.0  END
     ATOM  O2   TYPE OX2   CHARge  0.0  END
     ATOM  O3   TYPE OX2   CHARge  0.0  END
     ATOM  O4   TYPE OX2   CHARge  0.0  END

    BOND  S    O1
    BOND  S    O2
    BOND  S    O3
    BOND  S    O4

   { edit these DIHEdrals if necessary }

   { edit these IMPRopers if necessary }

   { edit these DONOrs and ACCEptors if necessary }
   ! DONOr H?  O1  ! only true if -OHx (x>0)
    ACCEptor  O1   S
   ! DONOr H?  O2  ! only true if -OHx (x>0)
    ACCEptor  O2   S
   ! DONOr H?  O3  ! only true if -OHx (x>0)
    ACCEptor  O3   S
   ! DONOr H?  O4  ! only true if -OHx (x>0)
    ACCEptor  O4   S

   END

    * the parameter file looks as follows:

   Remarks so4.par
   Remarks Created by XPLO2D V. 940816/1.2.1 at Mon Jan 16 22:43:20 1995 for user gerard
   Remarks Auto-generated by XPLO2D from file so4.pdb
   Remarks Parameters for residue type SO4

   set echo=false end

   { edit if necessary }
    BOND SX1  OX2    1250.0  1.506 ! Nobs =    4

   { edit if necessary }
    ANGLe OX2  SX1  OX2    1000.0   109.37 ! Nobs =    6

   { insert DIHEdrals yourself if necessary }
   { suggested weight = 300.0 for Engh & Huber compatibility }

   { edit if necessary }
    NONBonded SX1  0.0430  3.3676    0.0430  3.3676
    NONBonded OX2  0.1591  2.8509    0.1591  2.8509

   set echo=true end

• all you have to do now is to read the clean PDB file into O; draw the sulfate; move_zone into the density, and RSR_rigid to optimise the fit.