[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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