[gmx-developers] building block in rtp file

[Lakshmi Padmavathi]

Dear gromacs users,

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

so,i creatred one building block. i inserted in ffgmx.rtp, ffgmx.hdb and in
aminoacids.dat. i am using ffgmx forcefield ( option "0" of the forcefield)

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

for testing, i replaced the ALA (alanine) with YYY in rtpfile,hdb and 
aminoacid.dat file. i have given the alannin pdb coordinates. but it is still 
not recognising if i change just the name.

I am changing the residue name in pdb file also.

i request you all to give suggestion for this.

i will be very thankful to you. 

i will pastet he error of pdb2gmx here.

 
------------------------------------------------------------------------------------------------------
Opening library file /usr/local/share/gromacs/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 5 atoms

  chain  #res #atoms
  1 ' '     1      5

All occupancies are one
Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
 0: Gromacs Forcefield (see manual)
 1: Gromacs Forcefield with all hydrogens (proteins only)
 2: GROMOS96 43a1 Forcefield (official distribution)
 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
0
Using ffgmx force field
Opening library file /usr/local/share/gromacs/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file /usr/local/share/gromacs/top/ffgmx.rtp
Using default value - not generating all possible dihedrals
Using default value - excluding 3 bonded neighbors
Residue 97
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffgmx.hdb
Opening library file /usr/local/share/gromacs/top/ffgmx-n.tdb
Opening library file /usr/local/share/gromacs/top/ffgmx-c.tdb

Back Off! I just backed up test.top to ./#test.top.5#
Processing chain 1 (5 atoms, 1 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 1 donors and 1 acceptors
There are 1 hydrogen bonds
Fatal error: Residue 'YYY' not found in residue topology database


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=09 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