[gmx-users] questions about Topolbuild

[Tom]

Dear all

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 a amide group. It is strange for the same atom types. Some
atoms' potential can be assigned by Topolbuild but some can not.

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!


Thomos