The Molecular Dynamics Simulation of Peptides on Gold Nano-surfaces

User discussions
1

GROMACS version: 2022.1
GROMACS modification: Yes/No

Hello everyone! I’m currently working on simulating Gold Nanoparticles and Gold Nano/surfaces with peptides and I’m trying to recreate the tutorial of “The Molecular Dynamics Simulation of Peptides on Gold Nano-Surfaces”. I already created the box, the interaction with the peptide and make the solvatation with water molecules, but when i’m trying to run the energy minimization step this error appears to me:

atom name 1 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)
atom name 1 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 2 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 2 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 3 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 3 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 4 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 4 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 5 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 5 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 6 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 6 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 7 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 7 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 8 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 8 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 9 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 9 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 10 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 10 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 11 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 11 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 12 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 12 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 13 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 13 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 14 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 14 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 15 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 15 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 16 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 16 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 17 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 17 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU1)

atom name 18 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 18 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU2)

atom name 19 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 19 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU3)

atom name 20 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

atom name 20 in topol.top and AuLayer+peptide+water.gro does not match (AU - AU4)

(more than 20 non-matching atom names)

(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 2501]:
  800 non-matching atom names
  atom names from topol.top will be used
  atom names from AuLayer+peptide+water.gro will be ignored



-------------------------------------------------------
Program:     gmx grompp, version 2022.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2176)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate files
explicitly to avoid mistakes, although you can still use the same file as you
specify for the -c option.

I already try to change the name of the gold in the topology file base on the name of the .itp file, but it keeps giving me this error. Does anyone know how to handle this error? Thank you so much in advance.

I will leave the google drive link to look for all the files Au Simulation - Google Drive

2

Hello,
Are you simulate according to Danilo Roccatano’s paper?

3

Hi,

I usually get this type of error when the order of groups declared in the topology file ([ molecules ]) does not match the order of groups in the initial .gro/.pdb configuration.