[gmx-users] Error No Such Moleculetype System

[Justin Lemkul]

On 1/21/20 8:31 PM, Poncho Arvayo Zatarain wrote:
> Hello Gromacs users: im running the following command gmx grompp -p file.top -c solvated.gro -f minimization.mdp -o minimization.tpr but the following error appear: No such Molecule type system (line 16). I know this is about the topology, but i don see nothing strane in line 16. Line 16 is system. I hope can you help me. This is my topology:
> #include "martini_v2.2.itp"
>
>
>
> #include "Protein_A.itp"
> #include "Protein_B.itp"
>
> [ system ]
> ; name
> Martini system from 5iqp.pdb
>
> [ molecules ]
> ; name        number
> Protein_A 1
> Protein_B 1
> System           1008
> Protein          1008
> Protein-H        1008
> C-alpha          0
> Backbone         0
> MainChain        0
> MainChain+cb     0
> MainChain+H      0
> SideChain        1008
> SideChain+H      1008

What you have specified are default index groups, which are not 
[moleculetypes]. The only valid [moleculetype] directives are the ones 
found in the #included .itp files, which likely correspond to Protein_A 
and Protein_B.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================