[gmx-users] grompp fatal error in GROMACS version 4.5.7

[Justin Lemkul]

On 10/21/14 6:37 PM, Agnivo Gosai wrote:
> Dear GROMACS users
>
> I received the following error while running grompp to prepare the .tpr
> file before the initial energy minimization of my system.
>
>
>
>
>
>
> *Fatal error:Group DNA_chain_D referenced in the .mdp file was not found in
> the index file.Group names must match either [moleculetype] names or custom
> index groupnames, in which case you must supply an index file to the '-n'
> optionof grompp.*
> I used the following few commands in succession before this :-
> (1) pdb2gmx -f 1HAO.pdb -o complex.gro -p complex.top
> (2) editconf -f complex.gro -o complex_box.gro -bt dodecahedron -d 1.0
> (3) genbox -cp complex_box.gro -cs spc216.gro -p complex.top -o
> complex_solv.gro
> (4) grompp -f em.mdp -c complex_solv.gro -p complex.top -o ions.tpr
> (5) genion -s ions.tpr -o complex_ions.gro -p complex.top -pname NA -nname
> CL -neutral -conc 0.1
> (6) grompp -f em_real.mdp -c complex_ions.gro -p complex.top -o em.tpr
>
> After command (6) error is coming.
>
> In em.mdp file , at step (4) I have , "energygrps = system" and in
> em_real.mdp file at step (6) I have ," nenergygrps    = DNA_chain_D
> Protein_chain_L Protein_chain_H . ( Note : These files I gathered from Dr.
> Lemkuls tutorial on protein-ligand system )
>
> Also my complex.top file has the following :-
> ; Include chain topologies
> #include "complex_DNA_chain_D.itp"
> #include "complex_Protein_chain_L.itp"
> #include "complex_Protein_chain_H.itp"
> ...........................................................
> ...........................................................
> [ molecules ]
> ; Compound        #mols
> DNA_chain_D         1
> Protein_chain_L     1
> Protein_chain_H     1
> SOL         13578
> NA               39
> CL               28
>
> and ,
>
> "complex_DNA_chain_D.itp" has the following :-
> [ moleculetype ]
> ; Name            nrexcl
> DNA_chain_D         3
>
> Similar statements are available in the other two .itp files mentioned in
> the complex.top file. Now I am unable to understand what the error
> statement means by specifying "index file" ??
> Please shed some light upon this. I have also consulted the error section
> of the GROMACS documentation but could not understand.
>

The only valid groups without creating custom groups with an index file are 
listed here:

http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups

Names from [moleculetypes] are only used for things that are not listed in 
residuetypes.dat.  If you want separate energygrps for the two proteins and the 
DNA, you need to create an index file that defines those groups.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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