[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 18:09:50 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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