How to resolve the atom index out of bound error ın gromacs?

16 October 2023 2 2K Report

Dear All,

I am trying to simulate a dimer and would like to restrain a part of it on both chains. not a problem and the error is commonşy reported. so i tried all teh suggestions but none is working as grompp is accepting one of the posres files but throws the error for the other one. my toplogy file looks like this.

---------------

; Include chain topologies

#include "topol_Protein_chain_A.itp"

;; Include CRD Position restraint file for Chain A

#ifdef POSRES_CRD_A

#include "posre_crd_chain_A.itp"

#endif

#include "topol_Protein_chain_B.itp"

; Include CRD Position restraint file for Chain B

#ifdef POSRES_CRD_B

#include "posre_crd_chain_B.itp"

#endif

#include "topol_Ion_chain_A2.itp"

#include "topol_Ion_chain_B2.itp"

#include "topol_Protein_chain_A3.itp"

#include "topol_Protein_chain_B3.itp"

; Include water topology

#include "./charmm36-jul2022.ff/spce.itp"

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcx fcy fcz

1 1 1000 1000 1000

#endif

; Include topology for ions

#include "./charmm36-jul2022.ff/ions.itp"

[ system ]

; Name

2 Protein in water

[ molecules ]

; Compound #mols

Protein_chain_A 1

Protein_chain_B 1

Ion_chain_A2 1

Ion_chain_B2 1

Protein_chain_A3 1

Protein_chain_B3 1

SOL 111424

NA 48

--------------------

any suggestions are appreciated.

thank you

ayesha

Ayaz Anwar

The error is self-explanatory, like you are mentioning some atom which is not present in your gro file. can you share your mdp, gro and top files, and also the complete error from the terminal?

Ayesha Fatima

Dear Ayaz

Thank you for your answer. I was able to resolve the issue with the help from answers on GROMACS forum. the problem was in preparing the position restraint files using the original pdb files and using their atom indices.

Thank you so much for taking time to read my question

Best

Ayesha

Can someone help me with this error that I am getting while estimating a VAR model in R?

What are the easy methods or techniques to synthesize green nano particles?

For a PCR the volume of each component is standard ?

How can we know about the final concentration of each component to be used in the master mix for the PCR ?

A three level hierarchical data structure in multilevel modelling, for multiple response question?

How can I separate features and the background to measure pixel intensity?

Which are the appropriate metrics can be used to calculate overall Precision, Recall and F-measure in different data samples? and when can use F1?

How to convert Unit/mL enzyme concentration to FPU/mL or FPU/g concentration?

How can stem cells repair damaged cells?

How can to calculate the Computational complexity/cost (espatially, number of operations and space/memory cost) for an algorithm?

How to analyze a particular region of my simulation box in GROMACS?

How to get onecolumn document from standard IEEE ACCESS LateX template?

How can the modification of garden soil cause global warming?

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Does anyone know to clarify these changes?

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

How can I convert .vesta file to a .cif file?

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

How does GROMACS calculate the average structure of proteins?