Hello all,
I am facing an error when I use amber99 forcefield in Gromacs. I am not
aware on what may be the cause of the following error on a single strand
thymine. When I remove the P (phosphate) atom everything work without
problem. Since DNA contains P, I would like to know if anyone my advise me
on the way to proceed. I have also use the following amber forcefield (see
the website below) which was previously used in thyme repair calculation.
But I continue to have an error. If the file.rtp has to be modified, please
let me know.
http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/tutorial.html
the error obtained
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Reading thymine.pdb...
Read 63 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 3 chains and 0 blocks of water and 2 residues with 63 atoms
chain #res #atoms
1 'A' 2 40
2 ' ' 1 1
3 'A' 1 22
All occupancies are one
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/share/gromacs/top/amber99sb-ildn.ff/ffamber99o.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/resall.c, line: 150
Fatal error:
Atom type amber99_42 (residue HOH) not found in atomtype database
For more information and tips for troubleshooting, please check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thymine.pdb
ATOM 1 H5 T A 1 -0.423 -8.150 -2.094 1.00
0.00
ATOM 2 O5 T A 1 0.427 -7.826 -1.788 1.00
0.00
ATOM 3 C5 T A 1 1.443 -7.510 -2.756 1.00
0.00
ATOM 4 1H5 T A 1 1.100 -6.745 -3.453 1.00
0.00
ATOM 5 2H5 T A 1 1.674 -8.423 -3.305 1.00
0.00
ATOM 6 C4 T A 1 2.695 -7.020 -2.053 1.00
0.00
ATOM 7 H4 T A 1 3.574 -7.056 -2.696 1.00
0.00
ATOM 8 O4 T A 1 2.477 -5.630 -1.823 1.00
0.00
ATOM 9 C1 T A 1 2.308 -5.333 -0.452 1.00
0.00
ATOM 10 H1 T A 1 3.094 -4.693 -0.051 1.00
0.00
ATOM 11 N1 T A 1 1.098 -4.468 -0.370 1.00
0.00
ATOM 12 C6 T A 1 -0.158 -5.012 -0.400 1.00
0.00
ATOM 13 H6 T A 1 -0.280 -6.084 -0.439 1.00
0.00
ATOM 14 C5 T A 1 -1.255 -4.240 -0.327 1.00
0.00
ATOM 15 C7 T A 1 -2.636 -4.826 -0.358 1.00
0.00
ATOM 16 1H7 T A 1 -2.760 -5.509 0.482 1.00
0.00
ATOM 17 2H7 T A 1 -3.373 -4.026 -0.287 1.00
0.00
ATOM 18 3H7 T A 1 -2.780 -5.369 -1.292 1.00
0.00
ATOM 19 C4 T A 1 -1.141 -2.806 -0.214 1.00
0.00
ATOM 20 O4 T A 1 -2.087 -2.018 -0.141 1.00
0.00
ATOM 21 N3 T A 1 0.159 -2.344 -0.191 1.00
0.00
ATOM 22 H3 T A 1 0.296 -1.266 -0.105 1.00
0.00
ATOM 23 C2 T A 1 1.304 -3.113 -0.265 1.00
0.00
ATOM 24 O2 T A 1 2.414 -2.612 -0.237 1.00
0.00
ATOM 25 C3 T A 1 2.950 -7.607 -0.665 1.00
0.00
ATOM 26 H3 T A 1 2.586 -8.629 -0.554 1.00
0.00
ATOM 27 C2 T A 1 2.148 -6.679 0.247 1.00
0.00
ATOM 28 1H2 T A 1 1.344 -7.241 0.722 1.00
0.00
ATOM 29 2H2 T A 1 2.804 -6.267 1.014 1.00
0.00
ATOM 30 O3 T A 1 4.324 -7.545 -0.307 1.00
0.00
ATOM 31 P T A 2 4.728 -7.626 1.239 1.00
0.00
ATOM 32 O1P T A 2 6.009 -8.356 1.380 1.00
0.00
ATOM 33 O2P T A 2 3.592 -8.164 2.021 1.00
0.00
ATOM 34 O5 T A 2 4.945 -6.081 1.592 1.00
0.00
ATOM 35 C5 T A 2 5.582 -5.227 0.624 1.00
0.00
ATOM 36 1H5 T A 2 4.855 -4.809 -0.072 1.00
0.00
ATOM 37 2H5 T A 2 6.306 -5.829 0.075 1.00
0.00
ATOM 38 C4 T A 2 6.306 -4.095 1.327 1.00
0.00
ATOM 39 H4 T A 2 7.038 -3.607 0.684 1.00
0.00
ATOM 40 O4 T A 2 5.313 -3.099 1.557 1.00
0.00
ATOM 41 C1 T A 2 5.002 -2.958 2.928 1.00
0.00
ATOM 42 H1 T A 2 5.263 -1.978 3.329 1.00
0.00
ATOM 43 N1 T A 2 3.515 -2.969 3.010 1.00
0.00
ATOM 44 C6 T A 2 2.818 -4.148 2.980 1.00
0.00
ATOM 45 H6 T A 2 3.350 -5.087 2.941 1.00
0.00
ATOM 46 C5 T A 2 1.477 -4.168 3.053 1.00
0.00
ATOM 47 C7 T A 2 0.704 -5.454 3.022 1.00
0.00
ATOM 48 1H7 T A 2 1.005 -6.080 3.862 1.00
0.00
ATOM 49 2H7 T A 2 -0.362 -5.239 3.093 1.00
0.00
ATOM 50 3H7 T A 2 0.907 -5.978 2.088 1.00
0.00
ATOM 51 C4 T A 2 0.726 -2.941 3.166 1.00
0.00
ATOM 52 O4 T A 2 -0.502 -2.859 3.239 1.00
0.00
ATOM 53 N3 T A 2 1.506 -1.802 3.189 1.00
0.00
ATOM 54 H3 T A 2 0.984 -0.849 3.275 1.00
0.00
ATOM 55 C2 T A 2 2.884 -1.752 3.115 1.00
0.00
ATOM 56 O2 T A 2 3.489 -0.694 3.143 1.00
0.00
ATOM 57 C3 T A 2 6.858 -4.420 2.715 1.00
0.00
ATOM 58 H3 T A 2 7.164 -5.460 2.826 1.00
0.00
ATOM 59 C2 T A 2 5.664 -4.141 3.627 1.00
0.00
ATOM 60 1H2 T A 2 5.344 -5.069 4.102 1.00
0.00
ATOM 61 2H2 T A 2 5.952 -3.422 4.394 1.00
0.00
ATOM 62 O3 T A 2 7.933 -3.562 3.073 1.00
0.00
ATOM 63 H3 T A 2 8.313 -3.728 3.939 1.00
0.00
TER
Thank you for any suggestion
Collins
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Received on Fri Jul 05 2013 - 13:30:01 PDT
