[gmx-users] transfer pdb to gro

[He, Yang]

Hi all users,

When I use the editconf command to transform pdb file to gro file, it shows like this

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found

And this is my original pdb file

 ATOM   1  Ab   DNA           0.575    0.516     0.051   1.0  0.0
 ATOM   2  Tb   DNA           0.159    2.344     0.191   1.0  0.0
 ATOM   3  S1   DNA           2.365    6.568     1.280   1.0  0.0
 ATOM   4  S2   DNA           2.365   -6.568    -1.280   1.0  0.0
 ATOM   5  P1   DNA           -0.628   8.896     2.186   1.0  0.0
 ATOM   6  P2   DNA           -0.628  -8.896    -2.186   1.0  0.0
 ATOM   7  S3   DNA          -1.947    6.704    -4.660   1.0  0.0
 ATOM   8  S4   DNA          -1.947   -6.704     4.660   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5
CONECT  8  6
MASTER        0    0    0    0    0    0    0    0   8    0   8    0
END

not very complex, only 8 atoms .  And I find these atoms are not included in the gromacs so i defined them in the .atp file this

 Ab  134.1;   Adenine base of DNA
 Tb  125.1;   Thymine base of DNA
 S   83.11;   Sugar of DNA
 P   94.97;   Phosphate of DNA


 Can anyone of you help me sovle this problem?

Thank you in advance

Yang He