[gmx-users] how to add parameters to Topolbuild

[Tom]

Can someone help us about how to add misssing parameters
into Topolbuild?

We are using topolbuild to build *top file for a molecular which
has amide group.

Topolbuld reports missing parameters of bonding, angle and dihedral.
----------------------------
missing bond parameters of (C-N);
11 13 ; N7- C8
27 29 ; C6p- N9
45 47 ; N12p- C10

mising angle parameters of of CA-N-C, C-N-H, N-C-CA and N-C-O.:
7 11 13 ; C4- N7- C8
13 11 12 ; C8- N7- H7
11 13 14 ; N7- C8- C1p
11 13 23 ; N7- C8- O12

20 27 29 ; C5p- C6p- N9
29 27 28 ; N9- C6p- O13
27 29 30 ; C6p- N9- H9
27 29 31 ; C6p- N9- C7p

38 45 47 ; C11p- N12p- C10
47 45 46 ; C10- N12p- H12p
45 47 48 ; N12p- C10- C13p
45 47 57 ; N12p- C10- O18
-----------------------------------------
Even we manually add these paramters into the ffoplsaa.dat in the
default directory.
Topolbuild can recognized the bonds and angles but still can not write the
parameters onto *top file.

Thanks a lot for your help!

Happy New Year!

Thomos




After I have added the bond and angle parameters in to the ffoplsaa.dat,
the topolbuild still cannot give these data out.

The added parameters can be find in ffoplsaa.dat with the directory
/home1/02564/twei/HY/File/Polyamide/topolbuild1_3/dat/gromacs.

For bond,
;Added by HY on Dec 31, 2013 for polyamide in RO membrane
C N 1 0.133500 410032.0 ; from the OPLS AA.FF
for angle,
;Added by HY on Dec 31 2013 for polyamide in RO membrane.
CA C N 1 115.500 585.760 ;
O C N 1 120.400 669.440 ;
CA N C 1 121.900 418.400 ;
C N H 1 119.800 292.880 ;


missing parameters