[gmx-users] dihedral format in top file?

[Markus K. Dahlgren]

Hi,

I am inexperienced with gromacs and I would like to figure out the format of all
parts of a .top file, needed for Gromacs. I am trying to understand the input
format so I can write a program for automatic setup for small molecule ligands
with Gromacs, using the oplsaa force field. I have recently written a C++
program that converts BOSS autoput and creates NAMD input. Now I would like to
do a similar program for Gromacs.

I would like to write as few files as possible. I have some problems
understanding the format of the dihedrals in the .top file. I have pasted the
top file for methanol I have been preparing manually below. Please point out
any errors. Any pointers would be greatly appreciated.

Methanol    4

[atoms]
1  opls_157  1  UNK  C00  1  -0.043617
2  opls_154  1  UNK  O01  1  -0.586987
3  opls_156  1  UNK  H02  1   0.074589
4  opls_156  1  UNK  H03  1   0.074589
5  opls_156  1  UNK  H04  1   0.074589
6  opls_155  1  UNK  H05  1   0.406836

[bonds]
1  2  1  0.14100  267776.00
2  6  1  0.09450  462750.40
1  2  1  0.14100  284512.00
1  2  1  0.14100  284512.00
1  2  1  0.14100  284512.00

[angles]
4  1  2   1  109.50  292.880
5  1  2   1  109.50  292.880
6  2  1   1  108.50  460.240
3  1  2   1  109.50  292.880
4  1  5   1  107.80  276.144
5  1  3   1  107.80  276.144
5  1  4   1  107.80  276.144

[dihedrals]
6  2  1  3   3   ??
...              ??



If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how do I
enter the information in the dihedral part of the .top file? The RB parameters
for 6-2-1-3 is given below:

C0 = 0.94140
C1 = 2.82420
C2 = 0.00000
C3 = -3.76560
C4 = 0.00000
C5 = 0.00000

How do I enter this information into the .top file?

Any help would be greatly appreciated!

Thanks!
Best,
Markus