[gmx-users] how to add parameters to Topolbuild

[Bruce D. Ray]

On Wednesday, January 1, 2014 at 6:33 PM, Tom <dnaafm at gmail.com> wrote:
> 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.


First, topolbuild does not read the gromacs default directory
or the gromacs files.  Your command line had to give the
directory that contains topolbuild specific files
ATOMTYPE_OPLSAA1.DEF, ATOMTYPE_oplsaa.DEF and ffoplsaa.dat
Note that this ffoplsaa.dat is a special topolbuild specific
text file and not anything like the gromacs ffoplsaa.dat
However, this format is still text and can be edited with
a text editor.  To add parameters to this file, one must
know how many parameter lines are to be added to each type
of parameter.  At the top of each section is a descriptive
comment.  For bonds, that reads
     ; Bond lengths and forces
For angles, that reads
     ; angles phases and forces
Below each comment is a text line that gives a count.
For example
     bonds  258
or
     angles   789
Whenever entries are added or removed, this count must be
updated to reflect the current number of entries of that
type.  I use this count for memory allocation for the
assignment process. 

In what follows I will use the parameters you listed in
your message for the example.

At the bottom of the bonds entries add your bonds line
as (all one line):

C      N       1    0.133500       410032.0 ;                                             259

Then change the bonds count to 259
At the bottom of the angles entries, add your angles lines as
(4 lines):

CA     C      N      1   115.500    585.760   ;                                                   790
O      C      N      1   120.400    669.440   ;                                                   791
CA      N      C      1   121.900    418.400   ;                                                   792
C      N       H      1   119.800    292.880   ;                                                   793

Then change the angles count to 793

These edits to the topolbuild parameters file in
/your_topolbuild_directory/dat/gromacs/ffoplsaa.dat
should enable topolbuild 1.3.1 to put all the entries
into the topology.  Please remember to edit the *.top
file that results to reflect the change in location
of gromacs forcefield files that came with gromacs 4.*
because topolbuild 1.3.1 was written back when gromacs 3.3
was the current version.


> Thanks a lot for your help!

I hope this helps.


-- 
Bruce D. Ray, Ph.D. 
Associate Scientist 
IUPUI 
Physics Dept. 
402 N. Blackford St. 
Indianapolis, IN  46202-3273