# CHARMM-36 FF glycoprotein simulation: error no residue type find on rtp

**URL:** <https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [July 29, 2021, 6:21pm UTC](https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613 "2021-07-29T18:21:26Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![LaBiMM](https://avatars.discourse-cdn.com/v4/letter/l/c67d28/32.png) [@LaBiMM](https://gromacs.bioexcel.eu/u/LaBiMM)\
**Post date:** [July 29, 2021, 6:21pm UTC](https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613/1 "2021-07-29T18:21:26Z")

</div>

GROMACS version: 2020.6  
GROMACS modification: No  
Dear GMX users,  
I’d tried to simulate the SARS-COV-2 Spike glycoprotein obtained from CHAMM-GUI into GROMACS using charmm36-feb2021.ff.tgz (obtained from: [MacKerell Lab](http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs)) but on pdb2gmx I faced this error:  
[… many lines of information …]  
Opening force field file /opt/gromacs-2020.6/share/gromacs/top/charmm36-feb2021.ff/merged.arn

* * *

Program: gmx pdb2gmx, version 2020.6  
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)

## Fatal error: Atom N in residue BGLC 0 was not found in rtp entry BGLC with 24 atoms while sorting atoms. . 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)

CHARMM36 defines some building blocks (BGLC, BGLCA, BGLCA0, BGLCN0, BGLCNA) on _merged.rtp_ file and since _ **pdb2gmx** _ reads 3-long residue type characters (columns 18-20) and CHARMM36 presented 5 or 6-long residue name on merged.rtp file, so how can I correct assign these N-glycosilated residues on my protein generating my top files?  
Regards.

---

<div class="post-metadata">

**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 29, 2021, 6:46pm UTC](https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613/2 "2021-07-29T18:46:29Z")

</div>

CHARMM-GUI provides everything you need. You should not try to generate a topology within GROMACS. It can’t handle such complex glycoproteins. CHARMM-GUI also has a repository of prebuilt models for these systems.

---

<div class="post-metadata">

**Author:** ![LaBiMM](https://avatars.discourse-cdn.com/v4/letter/l/c67d28/32.png) [@LaBiMM](https://gromacs.bioexcel.eu/u/LaBiMM)\
**Post date:** [July 29, 2021, 7:25pm UTC](https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613/3 "2021-07-29T19:25:11Z")

</div>

Many thanks for you quick response Dr Justin!  
I saw the _COVID-19 Proteins Library_ at CHARMM-GUI site but I’m interested to simulate its soluble form (Fully-glycosylated full-length S protein complex models) available only on PDB format. I don’t want to run this membrane-embebbed protein, yet.  
I also tried to adapt the CHARMM-GUI GROMACS files (TOP, GRO) deleting the membrane, counter-ions,… but it required many text-file editions and it halted after 15 steps of position restrained steepest descent (curiously, the same step for membrane-embebbed protein!!).  
New tips will be a lot helpful!  
Regards.

---

<div class="post-metadata">

**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 29, 2021, 8:18pm UTC](https://gromacs.bioexcel.eu/t/charmm-36-ff-glycoprotein-simulation-error-no-residue-type-find-on-rtp/2613/4 "2021-07-29T20:18:52Z")

</div>

You should be able to build whatever you like using CHARMM-GUI starting from whatever protein coordinate file, since it can do complex things like add fly cans and handle the non-linear topology. My point is that `pdb2gmx` essentially can’t be used in this case (at least not in any easy way) so you need to generate all your inputs using CHARMM-GUI and at no point should you be trying to produce a topology using GROMACS tools.