GROMACS version: 2018.6
GROMACS modification: Yes
Hi Gromacs community, I have a question relating to the modification to a residue.rtp and want to clarify with the experts here. I am familiar with the fact that when I run pdb2gmx for a PDB file containing ACE-GLY-NME, gromacs will read amino acids.rtp to prepare a topology for my molecule. For glycine, its .rtp can look something like this:
[ bondedtypes ] ; mandatory
; bonds angles dihedrals impropers
1 1 1 2 ; mandatory
[ GLY ] ; mandatory
[ atoms ] ; mandatory
; name type charge chargegroup
N N -0.280 0
H H 0.280 0
CA CH2 0.000 1
C C 0.380 2
O O -0.380 2
[ bonds ] ; optional
;atom1 atom2
N H
N CA
CA C
C O
-C N
[ impropers ] ; optional
;atom1 atom2 atom3 atom4
N -C CA H
-C -CA N -O
Now let’s say I have a set of new bonded parameters that I only want to apply specific to glycine and not to any other amino acids, I can explicitly add the new bonded parameters like the below:
[ bondedtypes ] ; mandatory
; bonds angles dihedrals impropers
1 1 1 2 ; mandatory
[ GLY ] ; mandatory
[ atoms ] ; mandatory
; name type charge chargegroup
N N -0.280 0
H H 0.280 0
CA CH2 0.000 1
C C 0.380 2
O O -0.380 2
[ bonds ] ; optional
;atom1 atom2 b0 kb
N H 0.123 123456.7
N CA
CA C
C O 0.123 123456.7
-C N
[ angles ] ; optional
;atom1 atom2 atom3 th0 cth
N CA C 123.456 123.456
CA C O 123.456 123.456
[ dihedrals ] ; optional
;atom1 atom2 atom3 atom4 phi0 cp mult
N CA C O 0.0 1.23456 3
N CA C O 180.0 2.34567 2
N CA C O 0.0 3.45678 1
[ impropers ] ; optional
;atom1 atom2 atom3 atom4 q0 cq
N -C CA H 180.00 43.93200 2
-C -CA N -O 180.00 4.60240 2
My question is then: how does gromacs know which functional type to assign for these overwritten parameters to use (say, bond and angle are functype 1, dihedral are functype 9, and improper is functype 4) if I don’t specify it here? Unless, I can also explicitly specify the functional type for each bonded category here. If so, do I follow the same format as listed in ffbonded.itp?
Thank you very much for reading my messages!