Hello GROMACS users,
Because I am working on covalent bound ligands to serine, I have to create a .rtp file for GROMACS for a CHARMM-36 forcefield. I have found a .rtp file from a CHARMM-27 of a serine which is attached below.
I have a few questions.
Do I have to give all the coordinates of the ligand, or can I just give the coordinates of boron (since this is the only atom bound to serine)?
Are the charge and charge groups I copied from CHARMM-27.ff correct for the use of CHARMM-36?
[ SER ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
OG OH1 -0.66 7
HG1 H 0.43 8
C C 0.51 9
O O -0.51 10
[ bonds ]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OG HG1
O C
[ impropers ]
N -C CA HN
C CA +N O
There are no coordinates in an .rtp entry, as this is a topology. The .rtp entry must be a complete description of the molecule, not just a part of it.
If you’re parametrizing a species for CHARMM36, start with CHARMM36. I don’t know why you’d bother with an old version of the force field. But you can answer this question yourself simply by comparing the entries for SER in the two different force fields.
Dear Justin,
Sorry for my late reply. This is because I found a charmm27.ff folder in “gromacs/share/gromacs/top/” among the other forcefields available in Gromacs v2021.
Following the manual, I checked my mdp file produced with CHARMM-GUI and indeed it contains the required strings to use CHARMM36 except for “DispCorr = no”(https://manual.gromacs.org/documentation/2018/user-guide/force-fields.html):
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no
So my question is: since there is not a local charmm36.ff present in my local installation, should I simply download the one available from the MacKerell website (MacKerell Lab) and copy/paste the resulting unzipped charmm36-feb2021.ff in the gromacs/share/gromacs/top?
Dear Justin,
I have read some more topics in the forum about topology creation and I have done as follows to create my aminoacids with the whole compound:
I have drawn a serine covalently bound to my ligand using the graphical interface of Ligand Reader & Modeler of CHARMM-GUI server.
My first question here is: while designing the residue should I design it as a “free form” with a primary amine and a carboxylic acid rather than a NH and CO in a form of amide bond?
The resulting ser-ligand.itp contains the topology information. The format resembles the rtp file format but in comparison there are some differences. E.g., the atom block of the benzene ring of my covalent inhibitor has 8 columns instead of 4.
How do I convert this file to an .rtp file? For example the “type” column seems to be indexed with numbers while the template contains letters of the atoms.
Should I separate the chain containing the atoms of the inhibitor from those and call it “chain B” from those of the aminoacids “chain A”?
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG2R61 1 LIG C1 1 -0.115 12.0110 ; qtot -0.115
2 CG2R61 1 LIG C2 2 -0.127 12.0110 ; qtot -0.242
3 CG2R61 1 LIG C3 3 -0.112 12.0110 ; qtot -0.354
4 CG2R61 1 LIG C4 4 0.061 12.0110 ; qtot -0.293
5 CG2R61 1 LIG C5 5 -0.112 12.0110 ; qtot -0.405
6 CG2R61 1 LIG C6 6 -0.127 12.0110 ;
Template of Glycine:
[ 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
This is the only “official” source of CHARMM36 for GROMACS, so yes.
No, you shouldn’t be dealing with the backbone at all, since that is uniform for all amino acids. You should be parametrizing the side chain analog (terminating in a -CH3 group that is the analog of Cα.
