# Non-integer charges of arginine **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield\ **Created:** [March 15, 2021, 10:56pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757 "2021-03-15T22:56:47Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![rnd90](https://avatars.discourse-cdn.com/v4/letter/r/a8b319/32.png) [@rnd90](https://gromacs.bioexcel.eu/u/rnd90)\ **Post date:** [March 15, 2021, 10:56pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/1 "2021-03-15T22:56:47Z")
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](https://drive.google.com/file/d/17Nuo-cMZMa_s6FSN1f_cySLTwTotj2UY/view?usp=sharing) 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 ``` ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [March 16, 2021, 1:11pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/2 "2021-03-16T13:11:22Z")
You need to choose the “zwitterion” terminus types to get the correct patching for -NH3+/COO- forms, but I do not know if OPLS-AA supports neutral termini on isolated amino acids. ---
**Author:** ![rnd90](https://avatars.discourse-cdn.com/v4/letter/r/a8b319/32.png) [@rnd90](https://gromacs.bioexcel.eu/u/rnd90)\ **Post date:** [March 16, 2021, 7:09pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/3 "2021-03-16T19:09:56Z")
Hi Justin, Thank you so much!!! Do you happen to know why OPLS-AA does not support it by any chance? Is it because OPLS-AA was not originally designed for that, or was it simply has not been implemented in pdb2gmx? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [March 17, 2021, 1:34pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/4 "2021-03-17T13:34:08Z")
Fully neutral termini are not physically possible so a combination of NH2/COOH is not likely to be implemented in any force field, at least not for a zwitterion (a user could choose this for a polypeptide, but it would be physically incorrect). Anything that’s not supported is because there is no compelling reason to have it in a biomolecular force field, not that GROMACS elected to leave it out of the OPLS-AA implementation. ---
**Author:** ![rnd90](https://avatars.discourse-cdn.com/v4/letter/r/a8b319/32.png) [@rnd90](https://gromacs.bioexcel.eu/u/rnd90)\ **Post date:** [March 19, 2021, 10:38pm UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/5 "2021-03-19T22:38:41Z")
Justin, Yes, I agree that the combination of NH2/COOH should be rare. However, what do you think about NH2/COO? It is the third one from the left (“HB”) in the image below and should correspond to the pH level between 9 and 12 and q = 0. ![image (5)](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/7da88ff180671dfde0d76d2fd64298ba04fc2d28.png) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [March 20, 2021, 2:05am UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/6 "2021-03-20T02:05:55Z")
Zwitterions are supported in OPLS-AA because they are the most biologically relevant form of the species, and other combinations may or may not be supported depending on if both the N- and C-terminal patches require modification of the Cα charge. If they both do, they’re going to clash and lead to an incorrect topology. I certainly understand the chemistry quite well, but my point is force field developers spend time generating parameters that are likely to be widely used and will not necessarily cover every case. OPLS-AA may support the combination of NH2/COO-, so if that’s relevant to you, try it and see. ---
**Author:** ![tom.stavert](https://avatars.discourse-cdn.com/v4/letter/t/ac91a4/32.png) [@tom.stavert](https://gromacs.bioexcel.eu/u/tom.stavert)\ **Post date:** [July 3, 2021, 11:35am UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/7 "2021-07-03T11:35:42Z")
Hi @rnd90, I am facing the same issue and was wondering if you found managed to find a solution? Many thanks ---
**Author:** ![rnd90](https://avatars.discourse-cdn.com/v4/letter/r/a8b319/32.png) [@rnd90](https://gromacs.bioexcel.eu/u/rnd90)\ **Post date:** [July 4, 2021, 12:02am UTC](https://gromacs.bioexcel.eu/t/non-integer-charges-of-arginine/1757/8 "2021-07-04T00:02:20Z")
Hi Tom, I used OPLS-AA for q=+1 zwitterion. For example, if you need OPLS-AA arginine with +1 charge, then the command would be: ```auto echo 1 1 1 | gmx pdb2gmx -f arg_q1.pdb -o arg.gro -water spce -ff oplsaa -arg -ter ``` As for the neutral one, I postponed the simulation of it, but I vaguely remember I found the one in Amber or gromos force field. So the general recommendation is to explore carefully the options of pdb2gmx.