GROMACS version: 2021
GROMACS modification: No
Hi guys,
I have a question about setting a model of solvated arginine in water. Using the pdb2gmx util with OPLS-AA force field, I found out that the charges are not integers but some floating-point values with a ~0.1 delta from the desired value. For example, if I get an xyz file with arginine (I got it after optimization in Gaussian), convert it using babel, and then run:
# 1 -arg option value is for protonated arginine, i.e. arginine with q = +1
echo 1 | gmx pdb2gmx -f arg_q0_norm.pdb -o arg.gro -water spce -ff oplsaa -arg
It outputs me a correct structure (adds an extra proton to the amino group, making it NH3), but in the topology file the charges are set to 0.89, not 1.0.
For the neutral arginine, a similar command gives me a total charge of 0.1 (I expect exactly 0.0). I suspect that this is due to the fact that the original model was designed to be a part of a protein. Are there any flags or workaround to neutralize the system besides adding ions with the right proportion or setting a non-integer value on the ion charges? Thank you, any help is appreciated.
Here is the link to the whole archive
The topology file part for arginine with q = +1
; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ARG rtp ARG q +0.9
1 opls_287 1 ARG N 1 -0.3 14.0027
2 opls_290 1 ARG H1 1 0.33 1.008
3 opls_290 1 ARG H2 1 0.33 1.008
4 opls_290 1 ARG H3 1 0.33 1.008
5 opls_283 1 ARG CA 1 0.04 12.011
6 opls_140 1 ARG HA 1 0.06 1.008
7 opls_136 1 ARG CB 2 -0.12 12.011
8 opls_140 1 ARG HB1 2 0.06 1.008
9 opls_140 1 ARG HB2 2 0.06 1.008
10 opls_308 1 ARG CG 3 -0.05 12.011
11 opls_140 1 ARG HG1 3 0.06 1.008
12 opls_140 1 ARG HG2 3 0.06 1.008
13 opls_307 1 ARG CD 4 0.19 12.011
14 opls_140 1 ARG HD1 4 0.06 1.008
15 opls_140 1 ARG HD2 4 0.06 1.008
16 opls_303 1 ARG NE 5 -0.7 14.0067
17 opls_304 1 ARG HE 5 0.44 1.008
18 opls_302 1 ARG CZ 5 0.64 12.011
19 opls_300 1 ARG NH1 6 -0.8 14.0067
20 opls_301 1 ARG HH11 6 0.46 1.008
21 opls_301 1 ARG HH12 6 0.46 1.008
22 opls_300 1 ARG NH2 7 -0.8 14.0067
23 opls_301 1 ARG HH21 7 0.46 1.008
24 opls_301 1 ARG HH22 7 0.46 1.008
25 opls_271 1 ARG C 8 0.7 12.011
26 opls_272 1 ARG O1 8 -0.8 15.9994
27 opls_272 1 ARG O2 8 -0.8 15.9994 ; qtot 0.89