[gmx-users] about pdb2gmx and topology database

[nanyu101]

Hi,
  My molecule is polyester.I have created block topology as below:
[ ESF ]  ;The first block of my polyester
 [ atoms ]
     C1   CH2   0.000    4
     C2   C     0.180    2
     O1   OS   -0.360    2
     C3   CH2   0.180    2
     O2   OM    0.000    3
     C4   CH3   0.000    1

 [ bonds ]
 C1   +C4
 C4    C3
 C3    O1
 O1    C2
 C2    O
 C2    C1

 [ impropers ]
 C1    C2   O1    O2

[ EST ]  ; The block of my polyester
 [ atoms ]
 C1    CH2     0.000    1
 C2    C       0.180    2
 O1    OS     -0.360    2
 C3    CH      0.180    2
 O2    OM      0.000    3
 C4    CH3     0.000    4

 [ bonds ]
 C1   +C4
 C4    C3
 C3    O1
 O1    C2
 C2    O
 C2    C1

 [ impropers ]
 C1    C2   O1    O2

[ ESL ]  ; The last block of my polyester
 [ atoms ]
 C1    CH3     0.000    1
 C2    C       0.180    2
 O1    OS     -0.360    2
 C3    CH      0.180    2
 O2    OM      0.000    3
 C4    CH3     0.000    4

 [ bonds ]
 C1   +C4
 C4    C3
 C3    O1
 O1    C2
 C2    O
 C2    C1

 [ impropers ]
 C1    C2   O1    O2


But when I run pdb2gmx, the system told me wrong as below:
Reading pp.pdb...
Read 'C:\Wu\phb2.pdb  2002-12-11', 768 atoms
Opening library file /usr/local/gromacs/share/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Analyzing pdb file
There are 1 chains and 0 blocks of water and 128 residues with 768 atoms

  chain  #res #atoms
  1 ' '   128    768  

All occupancies are one
Opening library file /usr/local/gromacs/share/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/gromacs/share/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file /usr/local/gromacs/share/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/gromacs/share/top/ffgmx.hdb
Opening library file /usr/local/gromacs/share/top/ffgmx-n.tdb
Opening library file /usr/local/gromacs/share/top/ffgmx-c.tdb

Back Off! I just backed up pp.top to ./#pp.top.2#
Processing chain 1 (768 atoms, 128 residues)
Opening library file /usr/local/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'EST' not found in residue topology database



Would somebody give me some help?Thanks a lot.

Best,
Xianhui 

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