[gmx-users] Define a new residue in oplsaa

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Apr 14 18:45:27 CEST 2012


Dear GROMACS users,
I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE.
How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue?
I did like this, Is it correct?

[ ACE ]
 [ atoms ]
   CH3    opls_135   -0.180     1
  HH31    opls_140    0.060     1
  HH32    opls_140    0.060     1
  HH33    opls_140    0.060     1
     C    opls_235    0.500     2
     O    opls_236   -0.500     2
 [ bonds ]
   CH3  HH31
   CH3  HH32
   CH3  HH33
   CH3     C
     C     O
[ impropers ]
  CH3    +N    C      O     improper_O_C_X_Y 

[ FOR ]
 [ atoms ]
  HH31    opls_140    0.060     1
  HH32    opls_140    0.060     1
  HH33    opls_140    0.060     1
     C    opls_235    0.500     2
     O    opls_236   -0.500     2
 [ bonds ]
     C     O
[ impropers ]
  CH3    +N    C      O     improper_O_C_X_Y

Thanks in advance,
Shima
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