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

Jennifer Williams Jennifer.Williams at ed.ac.uk
Wed Jul 8 19:55:31 CEST 2009


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  

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?


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