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

[Justin Lemkul]

On 6/15/15 2:18 PM, Amanda Cameron wrote:
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> 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
>
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> 	
> 	
> 	
> 	ity of Lipid Membrane :
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>
> 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
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>
>
> The command pdb2gmx does not work.
>
> The error received was :
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> Program gmx, VERSION 5.0.2
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> 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
>
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> 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
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> How do we resolve this error?
>

pdb2gmx is for linear polymers with minimal branching.  Your coordinate file 
defines multiple AU in a single residue, but your .rtp says that there is one AU 
(which makes a bond definition impossible).  Note you need unique atom names in 
an .rtp file.  In any case, this is the wrong program entirely.  Try x2top.

-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

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