Lets say I have two residues which has dihedral angles defined by two different dihedral functions. One has functional form of proper dihedral(9) and other has a the form of Fourier dihedral (5).
But rtp allows specifying only one type of dihedral.
[ bondedtypes ]
1 1 9 2 0 3 1 1
where 9 is for proper dihedral.
Does anybody know to solve this problem?
I tried creating two different rtp files but it didn't work.
I get
Residues in one molecule have a different 'dihedrals' type: 9 and 5
Do you actually need to have this included in the .rtp file? After pdb2gmx, these functional form specifiers are then written in the .top file (or included there, in an .itp file), so there you can change them manually (or with a script) to whichever one you like.
Okay! I am currently doing it with a script. I just wanted to ask if there is a direct way to do it through Gromacs.
In this [ bondedtype ] header, you have this list that assigns functional forms to the respective entries:
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 5 9 2 1 3 1 0
Then you can have separate sections that specify e.g. bonds and impropers. I think in your case you could take, for instance, this [ all_dihedrals ] section (usually there's nothing interesting there), change its type to "5" in the header, and put your extra dihedral there. At least if it really makes a difference for you, it can be worth giving a try.
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