# GROMACS Full MD Setup error

**URL:** <https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145>\
**Category:** MDWeb\
**Created:** [July 1, 2021, 5:44pm UTC](https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145 "2021-07-01T17:44:30Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![vdvornyk](https://avatars.discourse-cdn.com/v4/letter/v/c2a13f/32.png) [@vdvornyk](https://ask.bioexcel.eu/u/vdvornyk)\
**Post date:** [July 1, 2021, 5:44pm UTC](https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145/1 "2021-07-01T17:44:30Z")

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Hello,  
During the setup, the following error is generated:

## Option Filename Type Description

-f 5\_162509376014205.gromacs.mdp Input, Opt! grompp input file with MD  
parameters  
-po mdout.mdp Output grompp input file with MD parameters  
-c 5\_162509376014205.gro Input Structure file: gro g96 pdb tpr tpb  
tpa  
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa  
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa  
-n 5\_162509376014205.ndx Input, Opt! Index file  
-p 5\_162509376014205.top Input Topology file  
-pp processed.top Output, Opt. Topology file  
-o 5\_162509376014205.tpr Output Run input file: tpr tpb tpa  
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt  
-e ener.edr Input, Opt. Energy file: edr ene

## Option Type Value Description

-[no]h bool no Print help info and quit  
-nice int 0 Set the nicelevel  
-[no]v bool yes Be loud and noisy  
-time real -1 Take frame at or first after this time.  
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual  
sites  
-maxwarn int 0 Number of allowed warnings during input processing  
-[no]zero bool no Set parameters for bonded interactions without  
defaults to zero instead of generating an error  
-[no]renum bool yes Renumber atomtypes and minimize number of  
atomtypes

checking input for internal consistency…

* * *

Program grompp\_sp, VERSION 4.0.2  
Source code file: grompp.c, line: 320

## Fatal error: No molecules were defined in the system

Any thought?  
Thank you.  
Volodymyr

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [August 28, 2021, 8:34am UTC](https://ask.bioexcel.eu/t/gromacs-full-md-setup-error/3145/2 "2021-08-28T08:34:49Z")

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Dear Volodymyr,

please sorry about the delay in answering your question, for some reason the automatic email wasn’t sent to me.

As your project is 2 months old because of our late response, I cannot track the error anymore, as temporary files have been automatically removed from the server. If you are still interested in the server, please try it again and get in contact with me, I will try to help you during the process.

Sorry again for the late reply.

Regards,

-Adam-