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

[Zhenting Gao]

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?

Thanks.           

　　　　　　　                    
　　　　　　　　　　                    

Yours sincerely,                    
Zhenting Gao                    
zhentg at 163.com                     
2004-11-3              

------------------------------------                    
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