[gmx-users] pdb2gmx adding a residue to the .rtp file
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 8 20:07:53 CEST 2009
Jennifer Williams wrote:
> I am trying to use the pdb2gmx to generate a .top file from my .pdb.
> I am getting the following error?.
> All occupancies are one
> Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.rtp
> Residue 56
> Program pdb2gmx, VERSION 4.0.5
> Source code file: resall.c, line: 138
> Fatal error:
> Atom type opls_23 (residue MCM) not found in atomtype database
> As my residue is not already present I have added the following to the
> end of the ffoplsaa.rtp file
> [ MCM ]
> [ atoms ]
> OH opls_23 -0.70 1
> HO opls_24 0.435 1
> SI SI 0.832 1
> OS opls_62 -0.400 1
> [ bonds ]
> SI OS
> SI OH
> OH HO
> [ dihedrals ]
> OS SI OH HO
> SI OS SI OS
> SI OS SI OH
> OH SI OH HO
> The following is already present in the ffoplsaabon.itp file (standard
> ; This bit added by DvdS for quartz simulation 2005-05-07
> ; These parameters are taken from GROMOS and were also used in
> ; Wensink et al. Langmuir 16 (2000) pp. 7392-7400
> [ bondtypes ]
> ; i j func b0 kb
> SI OS 1 0.16300 251040. ; From GROMACS
> SI OH 1 0.16300 251040. ;
> [ angletypes ]
> ; i j k func th0 cth
> SI OS SI 1 155.000 397.480
> OS SI OS 1 109.500 397.480
> OH SI OS 1 109.500 397.480
> SI OH HO 1 109.500 397.480
> [ dihedraltypes ]
> ; i j k l func coefficients
> ; Added DvdS for Quartz simulations
> SI OS 1 0.000 3.766 3
> SI OH 1 0.000 3.766 3
> And the entries in the .atp file which I am getting the error message
> about are already there (they are in the standard version-I didn?t need
> to add them myself). So I can?t figure out why they are not being read.
> I also tried adding the name of my residue (MCM) to aminoacids.dat and
> incrementing the count at the top.
> Do I need to make any other changes?
It looks fine. In theory you might want to edit the hdb file as wel if
you want to automatically add H, but I presume you have them already in
which case it is not necessary.
Which gromacs version are you using?
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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