# How to generate topology for a tripeptide molecule with protonation?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-generate-topology-for-a-tripeptide-molecule-with-protonation/10541>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [November 13, 2024, 2:09pm UTC](https://gromacs.bioexcel.eu/t/how-to-generate-topology-for-a-tripeptide-molecule-with-protonation/10541 "2024-11-13T14:09:01Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![vardhan](https://avatars.discourse-cdn.com/v4/letter/v/ebca7d/32.png) [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\
**Post date:** [November 13, 2024, 2:09pm UTC](https://gromacs.bioexcel.eu/t/how-to-generate-topology-for-a-tripeptide-molecule-with-protonation/10541/1 "2024-11-13T14:09:01Z")

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GROMACS version: 2023.5  
GROMACS modification: Yes  
I am trying to generate a topology file for a tripeptide molecule (Glutathione).  
As you know, it has Glycine, Cysteine, and Glutamic Acid.  
I built the pdb file by considering protonation for three groups  
1.) COO- (Glycine)  
2.) COO- (Gluta)  
3.) NH3+ (Gluta)

Also, in my PDB file I specified the atomnames as per the OPLS forcefield.  
I looked at the aminoacid.rtp file for the atomnames. A random residue name was assigned in the PDB file, by me.

I ran x2top (instead of pdb2gmx) with OPLS in -ff option (copied it to my working directory). I got the following errors.

"_WARNING: all CONECT records are ignored_  
_Opening force field file ./oplsaa.ff/atomname2type.n2t_

_There are 23 name to type translations in file ./oplsaa.ff_

_Generating bonds from distances…_  
_Can not find forcefield for atom NZ-1 with 4 bonds_  
_Can not find forcefield for atom CA-3 with 4 bonds_  
_Can not find forcefield for atom CG-5 with 3 bonds_  
_Can not find forcefield for atom CA-19 with 4 bonds_  
_Can not find forcefield for atom CB-23 with 3 bonds_  
_Can not find forcefield for atom SG-24 with 0 bonds_  
_Can not find forcefield for atom HG-25 with 0 bonds_  
_Can not find forcefield for atom CA-30 with 4 bonds_  
_Can not find forcefield for atom CG-31 with 3 bonds_

_Fatal error:_  
_Could only find a forcefield type for 27 out of 36 atoms_"

I am a beginner to GROMACS. I tried searching the topics and the documentation. But couldnt understand. Requesting your help. Thanks