[gmx-users] pdb2gmx adding a residue to the .rtp file

[David van der Spoel]

Jennifer Williams wrote:
> Hi,
> 
> 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 
> version);
> 
> ; 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?
> 
> Thanks
> 
> 
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