[gmx-users] dioxane

[Anthony Cruz]

Hi gromacs users:

I try to generate a dioxane box for use as solvent with the gromos FF. I try 
the PRODRG server and the charges looks wrong. How I can fix the charges?
Is good aproach to determine the charge wit gaussian (chelpg)???


;       
;       
;       This file was generated by PRODRG version 050304.0528
;       PRODRG written/copyrighted by Daan van Aalten
;       
;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CS2     1  DRG     CAA     1    0.108  14.0270   
     2       CS2     1  DRG     CAB     1    0.108  14.0270   
     3        OS     1  DRG     OAC     1   -0.324  15.9994   
     4       CS2     1  DRG     CAD     1    0.108  14.0270   
     5       CS2     1  DRG     CAE     2    0.187  14.0270   
     6        OS     1  DRG     OAF     2   -0.187  15.9994   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   1    0.152    251040.0    0.152    251040.0 ;   CAA  CAB   
   1   6   1    0.144    251040.0    0.144    251040.0 ;   CAA  OAF   
   2   3   1    0.144    251040.0    0.144    251040.0 ;   CAB  OAC   
   3   4   1    0.144    251040.0    0.144    251040.0 ;   OAC  CAD   
   4   5   1    0.152    251040.0    0.152    251040.0 ;   CAD  CAE   
   5   6   1    0.144    251040.0    0.144    251040.0 ;   CAE  OAF   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CAA  CAD   
   2   5   1                                           ;   CAB  CAE   
   3   6   1                                           ;   OAC  OAF   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   2   1   6   1    109.5       284.5    109.5       284.5 ;   CAB  CAA  OAF   
   1   2   3   1    109.5       284.5    109.5       284.5 ;   CAA  CAB  OAC   
   2   3   4   1    109.5       334.7    109.5       334.7 ;   CAB  OAC  CAD   
   3   4   5   1    109.5       284.5    109.5       284.5 ;   OAC  CAD  CAE   
   4   5   6   1    109.5       284.5    109.5       284.5 ;   CAD  CAE  OAF   
   1   6   5   1    109.5       334.7    109.5       334.7 ;   CAA  OAF  CAE   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   6   1   2   3   1      0.0    5.9 3      0.0    5.9 3 ; dih   OAF  CAA  CAB  
OAC   
   2   1   6   5   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAB  CAA  OAF  
CAE   
   1   2   3   4   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAA  CAB  OAC  
CAD   
   5   4   3   2   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAE  CAD  OAC  
CAB   
   3   4   5   6   1      0.0    5.9 3      0.0    5.9 3 ; dih   OAC  CAD  CAE  
OAF   
   4   5   6   1   1      0.0    3.8 3      0.0    3.8 3 ; dih   CAD  CAE  OAF  
CAA