[gmx-users] Fatal error: Atom Au in residue SUF 1 not found in rtp entry with 1 atoms while sorting atoms.

Yongqiang Wang ywang525 at uwo.ca
Mon Jul 3 18:45:49 CEST 2006


I want to do simulation with a model: some molecules  on Au(111) surface.
For convenient I construct 3 residues called " SHL, Auf, AuB", which mean
molecular, the surface gold atom, the deeper layer gold atoms. So I apend
the following lines to ffgmx.rtp file:

[ SHL ]

 [ atoms ]

     FA    F  -0.5  0

     FB    F  -0.5  0

     FC    F  -0.5  0

     CT    C   1.2  0

     CB    C  -0.3  1

     HB1   H   0.2  1

     HB2   H   0.2  1

     S     S   0.1  2             

 [ bonds ]

    FA    CT

    FB    CT

    FC    CT

    CT    CB

    HB1   CB

    HB2   CB

    CB    S

 [ angles ]

    CT    CB   S

 

[ SUF ]                 

 [ atoms ]              

    Auf   Au  0.05     0

  

[ SUB ]                 

 [ atoms ]              

Aub   Au  0.00     0

 

And add Au atom to ffgmx.atp file by the line:

   Au  196.96654;           gold

 

Then include the gold.itp file to ffgmx.itp, which includes the non-bonded
force field of gold atom. The following line is added to the ffgmx.itp file

#include "gold.itp"

 

And gold.itp file is

[ atomtypes ]

;name        mass      charge     ptype            c6           c12;
Universal Force Fields

    Au   196.9665         0.14     A     0.4164E-03     0.26549E-06;
large bases top Au

    Sc     196.9665           0.0        V     0.4164E-03     0.26549E-06;
large bases Bridge center Au

  [ bondtypes ]

  ; i    j func      b0          D      beta

    S    Au    3   0.2273    111.955    23.01

    Sc   Au    3   0.1962    237.81     13.97

[ angletypes ]

  ; i    j    k func       th0         cth

   Au    S    C  2        105.9      2011.85

   Sc    S    C  2        110.8      898.127

[ dihedraltypes ]

  Au S C C       3  6.11273  0.0       -3.30272  0.0       0.0         0.0

  Sc S C C       3  2.57279  0.0       -1.39008  0.0       0.0         0.0

 

My model pdb file is:

REMARK   Generated by pdbfile at yqwang in Jun,2006

REMARK Generated by vasp2pdb at yqwang

REMARK Box Vectors are following

REMARK  17.2676        0        0

REMARK        0   4.9847        0

REMARK        0        0       30

REMARK

CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1

MODEL      200 

ATOM  1     Au   SUF  1       8.343   2.280   4.333   1.00  0.00     Au  

ATOM  2     Au   SUF  2       5.162   2.235   4.421   1.00  0.00     Au  

ATOM  3     Au   SUF  3       2.410   2.243   4.381   1.00  0.00     Au  

ATOM  4     Au   SUF  4       -0.333  2.259   4.384   1.00  0.00     Au  

ATOM  5     Au   SUF  5       -3.431  2.184   4.453   1.00  0.00     Au  

ATOM  6     Au   SUF  6       -6.181  2.276   4.281   1.00  0.00     Au  

ATOM  7     Au   SUF  7       6.725   -0.430  4.241   1.00  0.00     Au  

ATOM  8     Au   SUF  8       3.890   -0.268  4.477   1.00  0.00     Au  

ATOM  9     Au   SUF  9       0.905   -0.248  4.329   1.00  0.00     Au  

ATOM  10    Au   SUF  10      -1.933  -0.456  4.193   1.00  0.00     Au  

ATOM  11    Au   SUF  11      -4.725  -0.307  4.457   1.00  0.00     Au  

ATOM  12    Au   SUF  12      -7.689  -0.233  4.417   1.00  0.00     Au  

ATOM  13    Au   SUB  13      6.702   -1.989  1.874   1.00  0.00     Au  

ATOM  14    Au   SUB  14      3.850   -1.952  1.965   1.00  0.00     Au  

...............

 

ATOM  46    Au   SUB  46      -1.939  -0.292  -3.049  1.00  0.00     Au  

ATOM  47    Au   SUB  47      -4.817  -0.292  -3.049  1.00  0.00     Au  

ATOM  48    Au   SUB  48      -7.695  -0.292  -3.049  1.00  0.00     Au  

ATOM  49    CT   SHL  49      -1.848  0.450   8.712   1.00  0.00     C   

ATOM  53    CB   SHL  49      -1.935  1.705   7.893   1.00  0.00     C   

ATOM  57    FA   SHL  49      -2.274  0.670   9.991   1.00  0.00     F   

ATOM  61    FB   SHL  49      -2.647  -0.540  8.209   1.00  0.00     F   

ATOM  65    FC   SHL  49      -0.578  -0.048  8.784   1.00  0.00     F   

ATOM  69    HB1  SHL  49      -2.902  2.171   8.078   1.00  0.00     H   

ATOM  73    HB2  SHL  49      -1.130  2.386   8.174   1.00  0.00     H   

ATOM  77    S    SHL  49      -1.796  1.293   6.111   1.00  0.00     S   

.... 

ATOM  52    CT   SHL  52      2.369   -1.447  8.926   1.00  0.00     C   

ATOM  56    CB   SHL  52      2.591   -0.107  8.290   1.00  0.00     C   

ATOM  64    FA   SHL  52      1.262   -2.114  8.490   1.00  0.00     F   

ATOM  68    FB   SHL  52      3.431   -2.296  8.734   1.00  0.00     F   

ATOM  60    FC   SHL  52      2.211   -1.293  10.279  1.00  0.00     F   

ATOM  72    HB1  SHL  52      1.867   0.586   8.724   1.00  0.00     H   

ATOM  76    HB2  SHL  52      3.597   0.217   8.560   1.00  0.00     H   

ATOM  80    S    SHL  52      2.389   0.088   6.471   1.00  0.00     S   

ENDMDL

Then I try to generate gro and top file by

pdb2gmx -f thiolau.pdb -o thiolau.gro -p thiolau.top

 

Followed lines are parts of the output of this command. I can not figure out
what is wrong the the steps, field definitions, or  models. 

I am a new user of Gromacs, Do me a favor to help me out, thank you so much.


...

Opening library file D:\Program\Gromacs321\gromacs\share\top\FF.dat

Select the Force Field:

 0: GROMOS96 43a1 Forcefield (official distribution)

 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)

 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)

 3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

 4: Gromacs Forcefield (see manual)

 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)

4

Looking whether force field file ffgmx.rtp exists

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx.rtp

Opening library file D:\Program\Gromacs321\gromacs\share\top\aminoacids.dat

Reading thiolau.pdb...

Read 80 atoms

Opening library file D:\Program\Gromacs321\gromacs\share\top\xlateat.dat

23 out of 23 lines of xlateat.dat converted succesfully

Analyzing pdb file

There are 1 chains and 0 blocks of water and 52 residues with 80 atoms

  chain  #res #atoms

  1 ' '    52     80

All occupancies are one

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx.atp

Atomtype 54

Reading residue database... (ffgmx)

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx.rtp

Residue 101

Sorting it all out...

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx.hdb

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx-n.tdb

Opening library file D:\Program\Gromacs321\gromacs\share\top\ffgmx-c.tdb

Processing chain 1 (80 atoms, 52 residues)

Opening library file D:\Program\Gromacs321\gromacs\share\top\specbond.dat

5 out of 5 lines of specbond.dat converted succesfully

There are 0 donors and 0 acceptors

There are 0 hydrogen bonds

Fatal error: Atom Au in residue SUF 1 not found in rtp entry with 1 atoms
while sorting atoms

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