[gmx-users] Fatal error: Atom type AU (residue LIG) not found in atomtype database

[Amanda Cameron]

Hello, 

We are trying to simulate gold nanoparticles (which we called the residue LIG) and we are trying to add the gold parameters in GROMACS using opls or charmm. 
The parameters are obtained from the article Effect of Gold Nanoparticle on Structure
and Fluid


	
	
	
	ity of Lipid Membrane : 



	
	
	
	


AuNP
non-bonded parameters
[
atomtypes ]
;name
 at.num   mass      charge  ptype       c6           c12
Au
     79  0.000      0.000     A  0.0584122 3.85761e-05



The command pdb2gmx does not work. 

The error received was : 








Program gmx, VERSION 5.0.2

Source code file: /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/resall.c, line: 165

Fatal error:

Atom type AU (residue LIG) not found in atomtype database

For more information and tips for troubleshooting, please check the GROMACS


Here is a part of our pdb file: 
HETATM    1 AU   LIG     1      -6.120  -6.120  -4.080  1.00  0.00          Au  
HETATM    2 AU   LIG     1      -6.120  -6.120   0.000  1.00  0.00          Au  
HETATM    3 AU   LIG     1      -6.120  -6.120   4.080  1.00  0.00          Au  
HETATM    4 AU   LIG     1      -6.120  -4.080  -6.120  1.00  0.00          Au  
HETATM    5 AU   LIG     1      -8.160  -4.080  -4.080  1.00  0.00          Au  
HETATM    6 AU   LIG     1      -8.160  -2.040  -2.040  1.00  0.00          Au  
HETATM    7 AU   LIG     1      -6.120  -2.040  -4.080  1.00  0.00          Au  
HETATM    8 AU   LIG     1      -6.120  -4.080  -2.040  1.00  0.00          Au  
HETATM    9 AU   LIG     1      -8.160  -4.080   0.000  1.00  0.00          Au  
HETATM   10 AU   LIG     1      -8.160  -2.040   2.040  1.00  0.00          Au  
HETATM   11 AU   LIG     1      -6.120  -2.040   0.000  1.00  0.00          Au  


The following changes were made to the oplsa forcefield. 

In the residuetypes.dat file the following was added: 
LIG     Protein
AU      Ion 

In the aminoacids.rtp : 

[ LIG ]
 [ atoms ]
AU         opsl_966   0.0584122    0
 [ bonds ]
AU     AU 

In the atomtypes.atp : 
opls_966   196.96657 ; Au
LIG         196.96657  ; Gold 





How do we resolve this error? 

Thanks in advance, 
Amanda