[gmx-users] How to add a new atomtype to GMX library? Which files should be modified?

Zhenting Gao zhentg at 163.com
Thu Nov 4 18:12:53 CET 2004

Hi  gmx-users,                          

     I want to add a MN2+(manganese with 2 positive charge, not bonded ) to the Gromos96 43a1 FF library.        
     I modified the following files:        
          ffG43a1.atp, ffG43a1nb.itp, ffG43a1nb.rtp                  

     I add a line in the ffG43a1.atp:          
          MN2+  54.93800 ;     manganese (charge 2+)          

     Also add a line in ffG43a1nb.itp [ atomtypes ]:          
          MN2+     0.000      0.000     A  0.0004182025  9.4400656e-09             
     And several line in other parts of ffG43a1nb.itp.          

     Add some lines in ffG43a1nb.rtp        
      [ MN ]        
      ;Zhenting Gao added        
       [ atoms ]        
         MN  MN2+     2.00000     0        
       [ bonds ]        
       [ angles ]        
      ;  ai    aj    ak   gromos type        
       [ impropers ]        
      ;  ai    aj    ak    al   gromos type        
       [ dihedrals ]        
      ;  ai    aj    ak    al   gromos type        

     However, I noticed that 2 files, 'atommass.dat' and 'vdwradii.dat' are read during the making of a topology file. Need I add the atom weight and vdw radii into these 2 files?        



Yours sincerely,                            
Zhenting Gao                            
zhentg at 163.com                             

Drug Discovery and Design Center,                            
Shanghai Institute of Materia Medica,                            
Chinese Academy of Science                            
P.R. China                          
URL http://www.dddc.ac.cn/group/zhentg.htm                          

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