[gmx-users] building block-rtp

Lakshmi Padmavathi lpulagam at uos.de
Thu Sep 11 18:44:01 CEST 2003

Dear gromacs users,

i would like make one building block for a abnormal residue (not usual amino 
acid but has aminoacid properties).

i creatred one building block. i inserted in ffgmx.rtp, ffgmx.hdb and in 

but it couldnot recognise the file in rtp database when i run pdb2gmx.

i request you all to give suggestion for this.

i will be very thankful to you. 

i paste my building block here.

[ XXX ]
 [ atoms ]
     N     N  -0.280     0
     H     H   0.280     0
    CA   CH1   0.000     1
    CB   CH2   0.000     2
    S1     S   0.000     3
     S     S   0.000     4
    C9   CH2   0.000	 5
    C8   CH3   0.000     6
    C7   CH3   0.000     7
    C6   CH3   0.000     8
    C5   CH3   0.000     9
    C4    CB   0.110    10
    N1  NR5*   0.080    10
    OH     O  -0.300    10
    C1    CB   0.110    10
    C2    CB   0.000    11
    C3   CR5   0.000    12
     C     C   0.380     4
     O     O  -0.380     4
 [ bonds ]
     N     H
     N    CA
    CA     C
     C     O
    -C     N
    CA    CB
    CB    S1
    S1     S
     S    C9
    C9    C2
    C2    C3
    C3    C4
    C6    C4
    C5    C4
    C4    N1
    OH    N1
    C2    C1
    N1    C1
    C8    C1
    C1    C7
 [ impropers ]
     N    -C    CA     H
    -C   -CA     N    -O
    CA     N     C    CB
    N1    C1    OH    C4
    C2    C1    C3    C9
    C1    C7    C8    N1
    C4    N1    C5    C6

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