# Residues in one molecule have a different 'all dihedrals' type: 0 and 1

**URL:** <https://gromacs.bioexcel.eu/t/residues-in-one-molecule-have-a-different-all-dihedrals-type-0-and-1/4213>\
**Category:** User discussions\
**Created:** [May 25, 2022, 5:46pm UTC](https://gromacs.bioexcel.eu/t/residues-in-one-molecule-have-a-different-all-dihedrals-type-0-and-1/4213 "2022-05-25T17:46:13Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![l454025801](https://avatars.discourse-cdn.com/v4/letter/l/50afbb/32.png) [@l454025801](https://gromacs.bioexcel.eu/u/l454025801)\
**Post date:** [May 25, 2022, 5:46pm UTC](https://gromacs.bioexcel.eu/t/residues-in-one-molecule-have-a-different-all-dihedrals-type-0-and-1/4213/1 "2022-05-25T17:46:13Z")

</div>

Hello!

I am using Gromacs 2020 with Charmm36-jul2021. I want to simulate a molecule with peptide tails and hydrocarbon heads. I add the info to the **.rtp file** and **residuetype.dat.** But when I do pdb2gmx, it gives me the error:

```
                  Program: gmx pdb2gmx, version 2020.5
                  Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 896)
                  
                  Fatal error:
                  Residues in one molecule have a different 'all dihedrals' type: 0 and 1

```

I tested the hydrocarbon alone and the peptide alone, and both are working. But when I put them together, it fails. Also, I tried removing the [impropers] from the entry, but it still failed.  
I searched the forum and found a similar post. However, it did not solve my problem. Could you please help?

The entry I have for my hydrocarbon is:

[C12] ; Hydrocarbon head  
[atoms]  
CA CG331 -0.267 0  
CB CG321 -0.185 1  
CC CG321 -0.178 2  
CD CG321 -0.180 3  
CE CG321 -0.180 4  
CF CG321 -0.180 5  
CG CG321 -0.180 6  
CH CG321 -0.180 7  
CI CG321 -0.180 8  
CJ CG321 -0.180 9  
CK CG321 -0.070 10  
C CG2O4 0.200 11  
O OG2D1 -0.400 12  
;H HGR52 0.090 13  
HA1 HGA3 0.090 13  
HA2 HGA3 0.090 14  
HA3 HGA3 0.090 15  
HB1 HGA2 0.090 16  
HB2 HGA2 0.090 17  
HC1 HGA2 0.090 18  
HC2 HGA2 0.090 19  
HD1 HGA2 0.090 20  
HD2 HGA2 0.090 21  
HE1 HGA2 0.090 22  
HE2 HGA2 0.090 23  
HF1 HGA2 0.090 24  
HF2 HGA2 0.090 25  
HG1 HGA2 0.090 26  
HG2 HGA2 0.090 27  
HH1 HGA2 0.090 28  
HH2 HGA2 0.090 29  
HI1 HGA2 0.090 30  
HI2 HGA2 0.090 31  
HJ1 HGA2 0.090 32  
HJ2 HGA2 0.090 33  
HK1 HGA2 0.090 34  
HK2 HGA2 0.090 35  
[bonds]  
CA CB  
CA HA1  
CA HA2  
CA HA3  
CB CC  
CB HB1  
CB HB2  
CC CD  
CC HC1  
CC HC2  
CD CE  
CD HD1  
CD HD2  
CE CF  
CE HE1  
CE HE2  
CF CG  
CF HF1  
CF HF2  
CG CH  
CG HG1  
CG HG2  
CH CI  
CH HH1  
CH HH2  
CI CJ  
CI HI1  
CI HI2  
CJ CK  
CJ HJ1  
CJ HJ2  
CK C  
CK HK1  
CK HK2  
C O  
C +N  
[impropers]  
C CK +N O

---

<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [June 2, 2022, 7:50am UTC](https://gromacs.bioexcel.eu/t/residues-in-one-molecule-have-a-different-all-dihedrals-type-0-and-1/4213/2 "2022-06-02T07:50:09Z")

</div>

Hi,  
It seems that you have a similar dihedral in the molecule that occur twice. In one case an improper dihedral (type 2) is associated to it and in another case a proper dihedral (type 1).  
Since the problem occurs when you simulated the peptide-hydrocarbon system, I guess that one of the dihedrals related to the connection between the peptide and the hydrocarbon may be related to the issue.  
\Alessandra