[gmx-users] Problems with PHL in ffgmx.rtp

Sean Cory sean.cory at mail.mcgill.ca
Fri Oct 15 15:44:23 CEST 2004

I ran a simulation with a PHL residue and I noticed there was no bond between 
the HY and OY atoms. 
When looking at ffgmx.rtp I noticed that in the bonds list there was a HY1 OY 
bond. There is no HY1 in the atoms list. When HY1 is changed to HY it seems 
to work fine.
I'm new to gromacs, does anybody see anything wrong with the change? Is this 
the right thing to do?

Sean Cory

This is the original PHL entry in ffgmx.rtp

[ PHL ]
 [ atoms ]
     N     N  -0.280     0
     H     H   0.280     0
    CA   CH1   0.000     1
    CB   CH2   0.000     2
    CG    CB   0.000     3
   CD1   CR6  -0.140     4
   HD1   HCR   0.140     4
   CD2   CR6  -0.140     5
   HD2   HCR   0.140     5
   CE1   CR6  -0.140     6
   HE1   HCR   0.140     6
   CE2   CR6  -0.140     7
   HE2   HCR   0.140     7
    CZ   CR6  -0.140     8
    HZ   HCR   0.140     8
    CX   CH2   0.150     9
    OY    OA  -0.548     9
    HY    HO   0.398     9
 [ bonds ]
     N     H
     N    CA
    CA     CX
    CX     OY
    HY1     OY
    -C     N
    CA    CB
    CB    CG
    CG   CD1
    CG   CD2
   CD1   HD1
   CD1   CE1
   CD2   HD2
   CD2   CE2
   CE1   HE1
   CE1    CZ
   CE2   HE2
   CE2    CZ
    CZ    HZ
 [ impropers ]
     N    -C    CA     H
    -C   -CA     N    -O
    CA     N     C    CB
    CG   CD1   CD2    CB
   CD2    CG   CD1   CE1
   CD1    CG   CD2   CE2
    CG   CD1   CE1    CZ
    CG   CD2   CE2    CZ
   CD1   CE1    CZ   CE2
   CD2   CE2    CZ   CE1
   CD1   HD1    CG   CE1
   CD2   HD2    CG   CE2
   CE1   HE1   CD1    CZ
   CE2   HE2   CD2    CZ
    CZ    HZ   CE1   CE2

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