[gmx-users] add bonds in tdb

[Tong Xinjie]

Hi all,

I'm trying to add bond in tdb but why it can't write a complete thing into top file ?

;for PCA /CFA /SA
[PCAT]
 [ add ]
1 1 C5T C13 C12 C14
C 12.011 0.067 -1
1 5 H6T C5T C13 C12 C14
HC 1.008 0.064 -1
1 4 O3T C5T C13 H6T
OA 15.9994 -0.621 -1

[ bonds ]
C5T     C13     0.1520 5.4300e+06
C5T     H6T     0.1100 1.2100e+07
C5T     O3T     0.1430 8.1800e+06


The below it part of .top generated from pdb2gmx . The bond force constants are missing which are marked in red.

16    18     2    0.1400    8.5400e+06
   18    19     2   0.1520
   18    23     2    0.1400    8.5400e+06
   19    20     2    0.1100
   19    21     2    0.1430
   23    24     2    0.1090    1.2300e+07


Anyone knows how to solve it? Thanks in advance.