[gmx-users] pdb2gmx : treat CL as C

[Nilesh Dhumal]

here is all information. I attached  2 attachment to my privious mail. It
looks 2nd didn't come. Sorry. Here I am giving details.

I am using opls force field . I added "PCD" as residue name in
aminoacid.dat file.

pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter

i have attached input:dioxin.pdb, output:di.pdb and di.top

here I have pasted the parameters from .rtp  file.

 [ PCD ]
 [ atoms ]
    O  opls_186   -0.3088  1
   C2  opls_263    0.2336  2
   C3  opls_263    0.2336  2
   O4  opls_186   -0.3088  1
   C5  opls_263    0.2336  2
   C6  opls_263    0.2336  2
   C7  opls_263   -0.2325  2
   C8  opls_263    0.0907  2
   C9  opls_263    0.0908  2
  C10  opls_263   -0.2326  2
  C11  opls_263   -0.2326  2
  C12  opls_263    0.0907  2
  C13  opls_263    0.0907  2
  C14  opls_263   -0.2325  2
 CL1   opls_264   -0.0986  3
 CL2   opls_264   -0.0986  3
 CL3   opls_264   -0.0986  3
 CL4   opls_264   -0.0986  3
  H19  opls_146    0.1612  4
  H20  opls_146    0.1612  4
  H21  opls_146    0.1612  4
  H22  opls_146    0.1612  4

[ bonds ]
    O  C2
   C2  C3
   C3  O4
   O4  C5
   C5  C6
   C6   O
   C3  C7
   C7  C8
   C8  C9
   C9  C10
  C10   C2
  C5   C11
  C11  C12
  C12  C13
  C13  C14
  C14  C6
   C8  CL1
   C9  CL2
  C12  CL4
  C13  CL4
  C10  H19
   C7  H20
  C14  H21
  C11  H22



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