# 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:** 20\ **Page:** 1
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 4, 2022, 4:03am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/1 "2022-07-04T04:03:18Z")
Continuing the discussion from [Energy min grompp](https://gromacs.bioexcel.eu/t/energy-min-grompp/4396/5): I have converted the itp of my gutathione to rtp format and copied the pdb to my strucuture along with using edit conf to renumber the file with a repacement residue. When I try to convert the pdb I recieve a error ```auto Fatal error: Residue 175 named GSH of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ``` I checked and residue 175 is a TYR and I cant find any issue with my carbons besides the segmented structure. ![gsh](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/cb7fdf47b708b31f6b3144bd58de57d5143a99e2.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:** [July 7, 2022, 3:49am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/2 "2022-07-07T03:49:26Z")
The problem is with the GSH residue; the next residue in the sequence expects it to have a C atom to create bonds (e.g. `-C` in the TYR `.rtp` entry) and apparently it does not, so `pdb2gmx` cannot build the expected bonded structure. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 12:45am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/3 "2022-07-22T00:45:28Z")
OK. I went back and realized the source of my issue was the lack of labeling or missing labels when I convert my pdb to mol2 for cgenff. This issue would result in a str with atom names I dont recognize and cant configure into a proper rtp. I have since started over confirming my atomnames I added hydrogens to my residue amine group to satisfy cgenff .attype warning: monovalent nitrogen not supported;skipped molecule ![Screenshot from 2022-07-21 18-32-41](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/bb1921517fd745709c3d855e989dbd813cef64c9.png) ![Screenshot from 2022-07-21 18-32-35](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/7f9b5e0f41216b2c8c627cc7ff4821138bcce221.png) Then I removed the amine hydrogens in before using the python charmm2gmx script to create an itp (H02 and H12) which I am trying to turn to an rtp. gsh.rtp ```auto [GSH] ;Gutathionylated cysteine 3 [atoms] ; atomN type charge cgnr N NG321 -1.015 1 CA CG311 0.140 2 C CG321 -0.256 3 O OG312 -0.923 4 CB CG321 0.062 5 SG SG301 -0.238 6 C01 CG321 0.039 7 N01 NG2S1 -0.395 8 O01 OG2D1 -0.514 9 S01 SG301 -0.189 10 C02 CG311 -0.010 11 N02 NG2S1 -0.457 12 O02 OG2D1 -0.516 13 N03 CG2O1 -1.077 14 O03 OG2D1 -0.568 15 O04 OG311 -0.598 16 C05 CG2O1 0.536 17 O05 OG2D1 -0.548 18 C06 CG321 -0.078 19 O06 OG311 -0.553 20 C07 CG2O2 0.743 21 C08 CG321 -0.199 22 C09 CG321 -0.268 23 C10 CG311 0.326 24 C11 CG2O2 0.779 25 H16 HGA1 0.090 26 H21 HGA2 0.090 27 H01 HGA2 0.090 28 H02 HGA2 0.090 29 H03 HGA1 0.090 30 H04 HGP1 0.333 31 H05 HGA2 0.090 32 H06 HGA2 0.090 33 H07 HGA2 0.090 34 H08 HGA2 0.090 35 H09 HGA2 0.090 36 H10 HGP1 0.277 37 H11 HGA2 0.090 38 H12 HGA2 0.090 39 H13 HGA2 0.090 40 H14 HGA2 0.090 41 H15 HGP1 0.430 42 H17 HGP1 0.290 43 H18 HGPAM2 0.396 44 H19 HGA1 0.090 45 H20 HGPAM2 0.396 46 ``` do I need to also write the [bonds] ? I started to convert them from the itp but they dont make sense in that there are repeats and connections not present in the pdb. I dont fully understand how to read or write hdb so I based it off cys since the backbone matches ```auto GSH 4 1 1 HN N CA -C 1 5 HA CA N CB C 2 6 HB CB CA SG 1 2 HG1 SG CB HB1 ``` gmx pdb2gmx -f db\_2dwp\_gsh\_.pdb -o 2dwp\_gsh.gro * * * Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 469) Fatal error: in .rtp file in residue moleculetype at line: GSH 3 For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) ---
**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:** [July 22, 2022, 2:17am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/4 "2022-07-22T02:17:09Z")
> [@deebee](#): > > .attype warning: monovalent nitrogen not supported;skipped molecule This warning suggests something intrinsically wrong with your `.mol2` file that should be rectified before even thinking about proceeding. It means the bonded structure is wrong. > [@deebee](#): > > Then I removed the amine hydrogens in before using the python charmm2gmx script to create an itp I don’t understand this. You should never be making manual edits to coordinates or topologies at this point. > [@deebee](#): > > do I need to also write the [bonds] ? At the bare minimum, yes. Otherwise `pdb2gmx` has no idea how the molecule is connected and you’ll just get a bunch of atoms in space that aren’t actually bonded in any way. You’ll also need `[impropers]` if there are any to assign. > [@deebee](#): > > Fatal error: > in .rtp file in residue moleculetype at line: > GSH 3 I don’t see where this is coming from based on what you’ve provided, but there’s something syntactically wrong with the residue definition. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 2:57pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/5 "2022-07-22T14:57:27Z")
“attype warning: monovalent nitrogen not supported;skipped molecule” this was a warning I resolved by adding hydrogens to my nitrogen attached to my CA. I figured this was because of CGENFF’s intended use on ligands rather than individual members of a polypeptide. I was trying to match the other rtp files while satisfying CGENFF I will retry with a new model, the nitrogen in its correct trivalent form bonded to the Calpha and a hydrogen ![Screenshot from 2022-07-22 10-05-30](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b2c41c4a635fe40a5f3439fde9233722e5fc656f.png) It concerns me that the resulting mol2 file doesnt display the double bonded oxygens also can I use atom types to write the bonds of the rtp? here is the resulting rtp with bonds `[GSH] ;Gutathionylated cysteine 3 [atoms] ; atomN type charge cgnr N NG2D1 -0.498 1 CA CG311 0.104 2 C CG321 -0.279 3 O OG312 -0.923 4 CB CG321 0.012 5 SG SG301 -0.200 6 C01 CG321 0.041 7 N01 NG311 -0.673 8 O01 OG312 -0.873 9 S01 SG311 -0.220 10 C02 CG311 0.073 11 N02 NG311 -0.789 12 O02 OG312 -0.874 13 C03 CG311 -0.049 14 N03 NG321 -1.000 15 O03 OG312 -0.879 16 O04 OG311 -0.609 17 C05 CG311 0.030 18 O05 OG312 -0.878 19 C06 CG321 -0.016 20 O06 OG311 -0.606 21 C07 CG311 0.044 22 C08 CG321 -0.188 23 C09 CG321 -0.217 24 C10 CG311 0.172 25 C11 CG311 0.021 26 H12 HGP1 0.334 27 H17 HGA1 0.090 28 H23 HGA2 0.090 29 H24 HGA1 0.090 30 H25 HGA1 0.090 31 H26 HGA1 0.090 32 H27 HGA1 0.090 33 H01 HGA2 0.090 34 H03 HGA2 0.090 35 H04 HGA1 0.090 36 H05 HGPAM1 0.349 37 H06 HGA2 0.090 38 H07 HGA2 0.090 39 H08 HGA2 0.090 40 H09 HGA2 0.090 41 H10 HGA2 0.090 42 H11 HGPAM1 0.361 43 H13 HGA2 0.090 44 H14 HGA2 0.090 45 H15 HGA2 0.090 46 H16 HGA2 0.090 47 H18 HGP1 0.370 48 H19 HGP1 0.370 49 H20 HGPAM2 0.390 50 H21 HGA1 0.090 51 H22 HGPAM2 0.390 52 [bonds] N CA ; NG321 CG311 N H12 ; CG311 CG321 CA C ; CG311 CG321 CA CB ; CG311 HGP1 CA H17 ; CG321 OG312 C O ; CG321 HGA2 C H23 ; CG321 HGA1 C H16 ; CG321 SG301 CB SG ; CG321 HGA2 CB H09 ; CG321 HGA2 CB H10 ; SG301 SG301 SG S01 ; CG321 SG301 C01 S01 ; CG321 CG311 C01 C02 ; CG321 HGA2 C01 H01 ; CG321 HGA2 C01 H03 ; NG2S1 CG311 N01 C02 ; NG2S1 CG2O1 N01 C03 ; NG2S1 HGP1 N01 H05 ; OG2D1 CG2O1 O01 C03 ; CG311 CG2O1 C02 C05 ; CG311 HGA1 C02 H04 ; NG2S1 CG2O1 N02 C05 ; NG2S1 CG321 N02 C06 ; NG2S1 HGP1 N02 H11 ; OG2D1 CG2O1 O02 C05 ; CG2O1 CG321 C03 C08 ; NG321 CG311 C03 H24 ; NG321 HGA1 N03 C10 ; NG321 HGPAM2 N03 H20 ; OG2D1 CG2O2 N03 H22 ; OG311 CG2O2 O03 C07 ; OG311 HGP1 O04 C07 ; OG2D1 CG2O2 O04 H18 ; CG321 CG2O2 C05 H25 ; CG321 HGA2 O05 C11 ; CG321 HGA2 C06 C07 ; OG311 CG2O2 C06 H13 ; OG311 HGPAM2 C06 H14 ; CG321 CG321 O06 C11 ; CG321 HGA2 O06 H19 ; CG321 HGA2 C07 H26 ; CG321 CG311 C08 C09 ; CG321 HGA2 C08 H07 ; CG321 HGA2 C08 H08 ; CG311 CG2O2 C09 C10 ; CG311 HGPAM2 C09 H06 C09 H15 C10 C11 C10 H21 C11 H27 ` I dont know if the charge#s are correct. I copied them from the str, but they dont match the patterns of the residues in the charmmff rtp. I ran through pdb2gmx ```auto ------------------------------------------------------- Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165) Fatal error: Atom HN not found in rtp database in residue GSH, it looks a bit like H12 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` I took this as gmx expecting an HN for my backbone amine with the name HN so I renamed my H12 HN and re ran pdb2gmx ```auto Opening force field file ./charmm36-jul2021.ff/aminoacids.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Segmentation fault (core dumped) ``` thanks for your support through this ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 3:22pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/6 "2022-07-22T15:22:25Z")
going over the errors ```auto Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165) Fatal error: Atom HN not found in rtp database in residue GSH, it looks a bit like H12 ``` it seems like there is a process of confirming residues by locating the expected HN which my residue lacks. I changed H12 to HN in my rtp and pdb and reran ```auto ------------------------------------------------------- Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 873) Fatal error: Atom H in residue GSH 205 was not found in rtp entry GSH with 52 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` i added ingh option with the HN substitution and ```auto ------------------------------------------------------- Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165) Fatal error: Atom HA not found in rtp database in residue GSH, it looks a bit like HN For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` How can I resolve my HA HN and any other hydrogen bonding issue? are there specifed names for the backbone atoms of all residues that I need to adhere to when designing my GSH? ---
**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:** [July 22, 2022, 3:39pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/7 "2022-07-22T15:39:06Z")
Your molecule is essentially a polypeptide with an unusual linkage. That’s all glutathione is. I would name everything like a standard amino acid, using all the same nomenclature. Honestly, you can assign all the atom types and charges directly from existing residues rather than going through all this mess. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 4:25pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/8 "2022-07-22T16:25:51Z")
How would you do this? is there an easier way than transcribing all the cys and gly and Glu bonds first then combining them in no specific order and pulling the s-s from my gsh. Ive never written an rtp file and I dont know whats wrong with my current one. Im currently running pdb2gmx and correcting every hydrogen name it spits out as “not found in rtp” ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 4:29pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/9 "2022-07-22T16:29:28Z")
```auto ------------------------------------------------------- Program: gmx pdb2gmx, version 2022 Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165) Fatal error: Atom HG1 not found in rtp database in residue GSH, it looks a bit like HN For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` why is gmx trying to build cys from GSH HG1 is the hydrogen that caps the sulfur of cys but doesnt exist in my GSH ---
**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:** [July 22, 2022, 4:45pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/10 "2022-07-22T16:45:03Z")
> [@deebee](#): > > why is gmx trying to build cys from GSH HG1 is the hydrogen that caps the sulfur of cys but doesnt exist in my GSH Because your `.hdb` entry tells it to. But that entry is poorly constructed and shouldn’t be used because the atom names are not correct and it is incomplete. Pattern the Cys portion of GSH after the disulfide form of Cys in the force field. I would suggest leaving the other Cys moiety of the disulfide off of this molecule so it is treated as a normal part of the protein, and add on the GSH as a new entry in `specbond.dat`. It will make your life far easier. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 5:52pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/11 "2022-07-22T17:52:17Z")
I am following your instrucution. I am renaming the atom names and types from another entry with a disulfide bond. I deleted my hbd and am writing a new one Why is it that gmx cant read the hydrogens in my rtp or pdb? I rewrote my specbond.dat ```auto 9 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS SG 1 HEM FE 2 0.25 CYS2 HEME CYS SG 1 HEM CAB 1 0.18 CYS2 HEME CYS SG 1 HEM CAC 1 0.18 CYS2 HEME HIS NE2 1 HEM FE 1 0.2 HIS1 HEME MET SD 1 HEM FE 1 0.24 MET HEME CO C 1 HEME FE 1 0.19 CO HEME CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 GSH SG 1 GSH SD 1 0.2 GSH GSH ``` the formatting is correct in my file ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 22, 2022, 8:18pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/12 "2022-07-22T20:18:26Z")
I wrote a better hbd and edited my rtp here is my .gro ![Screenshot from 2022-07-22 16-13-38](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1e3f6c913389571fe9b199824b3696c336ddfb5f.png) I pushed it through pdb2gmx -ingh as to follow the hbd i wrote instead and it looks properly assembled. First off thank you for your help! my only question is how would you confirm the assembly? ---
**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:** [July 23, 2022, 2:24am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/13 "2022-07-23T02:24:02Z")
> [@deebee](#): > > my only question is how would you confirm the assembly? `grompp` finishes with no warnings and an energy minimization finishes with a sensible geometry. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 25, 2022, 1:57pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/14 "2022-07-25T13:57:38Z")
since completing my .gro i also added to the ffbonded.itp based on the gsh.prm and itp data. I have run into errors /w trying to add ion’s with grompp ```auto ERROR 1 [file topol.top, line 36837]: No default U-B types ERROR 2 [file topol.top, line 36838]: No default U-B types ERROR 3 [file topol.top, line 51480]: No default Proper Dih. types ERROR 4 [file topol.top, line 51481]: No default Proper Dih. types ERROR 5 [file topol.top, line 51482]: No default Proper Dih. types ERROR 6 [file topol.top, line 51483]: No default Proper Dih. types ERROR 7 [file topol.top, line 51484]: No default Proper Dih. types ERROR 8 [file topol.top, line 51485]: No default Proper Dih. types ERROR 9 [file topol.top, line 51486]: No default Proper Dih. types ERROR 10 [file topol.top, line 63449]: Unknown cmap torsion between atoms 2772 2814 2816 2824 2826 There was 1 note ------------------------------------------------------- Program: gmx grompp, version 2022 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1715) Fatal error: There were 10 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` I added my dihedrals from the created prm ( charmm2gmx) along with my bonds. How would you address these? also is there a helpful guide for adding to the ffnonbonded.itp? I looked over another discussion > [@Error in use of GROMPP](https://gromacs.bioexcel.eu/t/error-in-use-of-grompp/129/2): > > The missing parameters warnings indicate that parameters that **should** be in the ligand topology are not there. Check to make sure you haven’t edited those out inappropriately. and reading the info of the errors the top is listing contacts between my new residue and the backbone atomistic contacts that are missing description that should be covered in the dih types of the ffbonded.itp do i use similar entries to describe these dihedrals? for example ```auto ERROR 4 [file topol.top, line 51483]: No default Proper Dih. types ``` I see in the topology file ln 51483 2748 2766 2768 2770 9 which refers to the solv.gro 204LYS N 2746 10.735 7.696 4.086 204LYS HZ2 2764 10.981 7.390 4.350 204LYS C 2766 10.837 7.764 3.868 205GSH CA 2770 10.763 7.793 3.652 so i would look up another instance where lys is next to cys and add it to the ffbonded.itp? otherwise build a 3 peptide chain of the residues surrounding gsh and push it through cgen to copy the missing dihedrals? ---
**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:** [July 27, 2022, 3:38am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/15 "2022-07-27T03:38:38Z")
> [@deebee](#): > > I added my dihedrals from the created prm ( charmm2gmx) along with my bonds. How would you address these? Where did you add them? What are the lines you added? It is sufficient to `#include` a topology file that lists any new bonded parameters rather than necessarily hack `ffbonded.itp`. ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 27, 2022, 12:01pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/16 "2022-07-27T12:01:16Z")
Thank you. I thought that wouldnt work for residues the ligand topology from charmm doesnt match the rtp I wrote. I dont think I can just copy it over to my rtp because the backbone doesnt match would I be able to just add the itp and prm for the r-group since the bonded and nonbonded parameters of the backbone match cys (and should be already included) or do the parameters need to be specified. should I rewrite the rtp (mainly the r-group, keeping the cys-based backbone) and rerun pdb2gmx with the renamed retyped rtf and hbd (based on the charmmgui topology)? or could I just make the addition to the R-group a separate residue in the rtf and the hbd, break up the construction into 2 parts? Could I just change my cys to a disulfide cys2 and add my gutathione as a ligand? how would I describe this in my rtp and hbd? could I just write gutathione with a incomplete sulfur? ultimately i dont understand how to add my new residue topology parameters and coordninates to the protein. Also should I create a new residue to add in place of cys to insert into the protein or just a new R group to add as a covalent attachment ? currently I understand my errors are due to my bonded and nonbonded information missing from my top file in the form of prm and itp files ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 27, 2022, 4:08pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/17 "2022-07-27T16:08:28Z")
I went forward and wrote a new pdb with cys2 in place of ptm site i followed your protein ligand instructions in designing my gutathione as a ligand and using cgenff to parameterize it. after parameterization I removed the backbone atoms and converted it to a .gro i pasted it in to make my complex.gro Im having trouble customizing the itp to only represent the R group of my original structure. also how do i write this as covalently attached to cys2? I rewrote my specbonds.dat but how do i call for that to be applied in this .top ```auto ERROR 2 [file gsh3.itp, line 52]: Atom index (37) in bonds out of bounds (1-34). This probably means that you have inserted topology section "bonds" in a part belonging to a different molecule than you intended to. In that case move the "bonds" section to the right molecule. ``` currently I am correcting the bonds to only connect the remaining r group atoms ```auto [bonds] ; ai aj funct c0 c1 c2 c3 13 34 1 ; CG321 HGA2 **from atom 13 to 34 single bond?** 5 28 1 ; CG321 HGA2 7 9 1 ; CG311 NG2S1 7 18 1 ; CG311 CG2O1 7 26 1 ; CG311 CG321 7 37 1 ; CG311 HGA1 8 26 1 ; SG301 CG321 9 10 1 ; NG2S1 CG2O1 9 38 1 ; NG2S1 HGP1 10 11 1 ; CG2O1 CG321 10 12 1 ; CG2O1 OG2D1 11 13 1 ; CG321 CG321 11 41 1 ; CG321 HGA2 11 42 1 ; CG321 HGA2 13 14 1 ; CG321 CG311 13 43 1 ; CG321 HGA2 13 44 1 ; CG321 HGA2 14 15 1 ; CG311 NG321 ``` If my understanding is correct (above) how do I connect the SG301 of gsh to the SM of cys2? ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 27, 2022, 7:09pm UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/18 "2022-07-27T19:09:15Z")
Correct me if I’m wrong. I currently see 2 ways to build my structure. The recommended route of : building my alternative residue pdb, Formatting to determine the topology (cgenff), Then formatting the structure based on the topologies already provided in the gmx rtp (identify the names and types then replace the names types and bond information of the itp to match a traditional residue, for me I could see this working by replacing the backbone of gsh with atoms matching cys) paste the formatted itp in the rtp write up an hbd for new residue rewrite the .gro adding the coordinates of the gsh r group to the cys and renaming it GSH the other way which I am currently working is to change cys to cys2 with an available sulfur treat the R-group as a ligand convert the pdb to gro add it to the protein .gro build the pdb, format it to push through cgenff then remove the backbone change the sulfur to something indicating its attachment to the cys2 sulfur atom type sm in the ligand itp edit the $gmx top specbonds.dat to allow the bond. also could you help me understand the `[pairs]` section of the itp ```auto [pairs] ; ai aj funct c0 c1 c2 c3 1 4 1 1 30 1 1 31 1 1 6 1 1 35 1 1 36 1 2 32 1 2 8 1 ``` ---
**Author:** ![deebee](https://avatars.discourse-cdn.com/v4/letter/d/e56c9b/32.png) [@deebee](https://gromacs.bioexcel.eu/u/deebee)\ **Post date:** [July 28, 2022, 1:35am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/19 "2022-07-28T01:35:40Z")
Is there a better way than reading through the itp and looking up each line of atoms bonds and dihedrals to rewrite it and then rewrite it again when the numbers refering to the codes change? ---
**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:** [July 30, 2022, 2:49am UTC](https://gromacs.bioexcel.eu/t/new-residue-top/4405/20 "2022-07-30T02:49:08Z")
The simplest thing to do here is to simply create an all-in-one residue. Start with the disulfide Cys and build out from the backbone by adding the γ-Glu-Cys(disulfide form)-Gly. Pretty much all the bonded connectivity and associated `.hdb` information comes directly from the existing residues. The only difference is the γ-peptide bond, but you can take all the charges and atom types from the backbone of existing residues. There may be a missing dihedral or two, but those are simple to introduce by analogy. [Next page](https://gromacs.bioexcel.eu/t/new-residue-top/4405.md?page=2)