# New residue top **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, simulation-setup\ **Created:** [July 4, 2022, 4:03am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405 "2022-07-04T04:03:18Z")\ **Posts on this page:** 6\ **Page:** 2
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [August 3, 2022, 3:20pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/21 "2022-08-03T15:20:12Z")
can you explain “introduce by analogy”? am I correct in understanding I can build the RTP from cys glu and gly along with adding for the S-S atoms which I can find in the atomtypes file? then if I used the atom types of traditional AA i should only have at most a few dihedrals to address which I can write by looking through the ffbonded file and finding a similar set of bonds applying my specific atom types to add to my missing dihedrals.itp ---
**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:** [August 6, 2022, 1:56pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/22 "2022-08-06T13:56:36Z")
> [@deebee](#): > > can you explain “introduce by analogy”? Look at existing residues and assign the same atom types and charges for chemically equivalent (or sufficiently similar moieties). > [@deebee](#): > > am I correct in understanding I can build the RTP from cys glu and gly along with adding for the S-S atoms which I can find in the atomtypes file? Yes. > [@deebee](#): > > then if I used the atom types of traditional AA i should only have at most a few dihedrals to address which I can write by looking through the ffbonded file and finding a similar set of bonds applying my specific atom types to add to my missing dihedrals.itp Correct. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [August 15, 2022, 7:56pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/23 "2022-08-15T19:56:26Z")
I rewrote my rtp exclusively using atom types from glu asp gly cys as to avoid writing new bonded parameters ```auto ;Gutathionylated cysteine +1 [atoms] N NH1 -0.6300 1 HN0 H 0.3600 2 CA CT1 0.3310 3 HA HB1 0.0000 4 CB CT2 0.2300 5 HB1 HA2 0.0000 6 HB2 HA2 0.0000 7 SG SM -0.2300 8 SD SM -0.2300 9 CY CT2 0.2300 10 HY1 HA2 0.0000 11 HY2 HA2 0.0000 12 CD CT1 0.5640 13 ; aliphatic C with 1 H, CH HD HB1 0.0000 14; alkane, CH, NB NH3 -0.7990 15 HN1 H 0.4500 16 HN2 H 0.4500 16 CE C 0.9050 17 ; carbonyl C: [negative] carboxylates OE O -0.5700 18 ; carbonyl O: negative groups: carboxylates, carbonate CF CT2 0.0610 19 ;ch2 HF1 HA2 0.0000 20 ;alphatic proton, CH2 HF2 HA2 0.0000 22 ;alphatic proton, CH2 CH CT2 0.0000 23 ;ch2 HH1 HA2 0.0000 24 ;alphatic proton, CH2 HH2 HA2 0.0000 25 ;alphatic proton, CH2 CM CT1 0.3970 26 ; aliphatic sp3 C for CH HG HA1 0.0000 27 ; alphatic proton, CH NY NH3 -0.8530 28; ammoniumide nitrogen HN3 HC 0.4500 29 ; polar H HN4 HC 0.4500 30 ; polar H HN5 HC 0.4500 31 CJ C 0.9060 32 ; carbonyl C: [negative] carboxylates OF OC -0.9000 33 ; carbonyl O: negative groups: carboxylates, carbonate OG OC -0.9000 34 ; carbonyl O: negative groups: carboxylates, carbonate CL C 0.9050 35 ; carbonyl C: [negative] carboxylates OI O -0.5700 36 ; carbonyl O: negative groups: carboxylates, carbonate NZ NH3 -0.7990 37 HZ1 H 0.4500 38 HZ2 H 0.4500 39 CQ CT2 0.3970 40 ;ch2 HQ1 HA2 0.0000 41 ;alphatic proton, CH2 HQ2 HA2 0.0000 42 ;alphatic proton, CH2 CZ C 0.9060 43 ; carbonyl C: [negative] carboxylates OM OC -0.9000 44 ; carbonyl O: negative groups: carboxylates, carbonate ON OC -0.9000 45 ; carbonyl O: negative groups: carboxylates, carbonate C C 0.5090 46 O O -0.5700 47 [bonds] CB CA SG CB N HN0 N CA C CA C +N CA HA CB HB1 CB HB2 CB SG SG SD SD CY CY HY1 CY HY2 CY CD CD HD CD NB CD CL NB HN1 NB HN2 NB CE CE OE CE CF CF HF1 CF HF2 CF CH CH HH1 CH HH2 CH CM CM HG CM NY CM CJ NY HN3 NY HN4 NY HN5 CJ OF CJ OG CL OI CL NZ NZ HZ1 NZ HZ2 NZ CQ CQ HQ1 CQ HQ2 CQ CZ CZ OM CZ ON O C [impropers] N -C CA HN C CA +N O CL NZ CD OI ; carbonyl c CL CD NZ OI ;carbonyl c CZ CF ON OM ; carboxylic CJ CM OG OF ; carboxylic CE CF NB OE; carbonyl c CE NB CF OE; carbonyl c [cmap] -C N CA C +N ``` I am able to assemble my .gro but when I try to run gromp to make my ions.tpr there are 65 errors about missing bonded and unbonded and dihedrals. ```auto ERROR 1 [file topol.top, line 10020]: No default Bond types ERROR 26 [file topol.top, line 36965]: No default U-B types ERROR 63 [file topol.top, line 51688]: No default Proper Dih. types Fatal error: There were 65 errors in input file(s) ``` I believe this is refering to the bonds pairs angles and dihedrals that are produced by swissparam or cgenff. How would you advise I resolve these errors. is there a simpler way than addressing all 65 one by one finding the match in the topol then looking it up in the .gro then matching it to my itp and entering it in my ffbonded.itp one by one? ---
**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:** [August 18, 2022, 10:54am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/24 "2022-08-18T10:54:21Z")
If you’re using all standard residue definitions and atom types from CHARMM, I have no idea how CGenFF or SwissParam would even factor in here. Aren’t you using `pdb2gmx` to produce the entire topology once you have written the `.rtp` entry? ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [August 18, 2022, 11:12am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/25 "2022-08-18T11:12:11Z")
Yes, I used pdb2gmx. I used swissparam to determine charges as to avoid a qtot that is a float when assembling my rtp. ---
**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:** [August 18, 2022, 4:01pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/26 "2022-08-18T16:01:46Z")
You should be getting the charges from the existing residue definitions, but even so, the charge assignment has nothing to do with missing bonded parameters, which I find odd. Please report back about what a few of the missing bonds are. [Previous page](https://gromacs.bioexcel.eu/t/new-residue-top/4405.md?page=1)