[gmx-users] Fatal error: Atomtype 'OS' not found!

[Yunfeng Hu]

In fact that is what I did. Here is what my topology file looks like:
;
;       File '7a1.top' was generated
;       By user: yunfenghu (501)
;       On host: Yunfeng-Hus-Computer.local
;       At date: Thu Sep 30 17:46:23 2004
;
;       This is your topology file
;       "Uh-oh .... Right Again" (Laurie Anderson)
;
; Include forcefield parameters
#include "ffG43a1.itp"
#include "cocaine.itp"

[ moleculetype ]
; Name            nrexcl
Protein_L           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
typeB    chargeB      massB
      1         NL      1    ASP      N      1      0.129    14.0067   ; 
qtot 0.129
      2          H      1    ASP     H1      1      0.248      1.008   ; 
qtot 0.377
      3          H      1    ASP     H2      1      0.248      1.008   ; 
qtot 0.625
      4          H      1    ASP     H3      1      0.248      1.008   ; 
qtot 0.873
......
[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_L           1
COC                 1
SOL              6502

On Oct 6, 2004, at 12:52 AM, Daan van Aalten wrote:

>
> Hi
>
> You have to manually edit the complex.top to include the #include
> statement as explained in detail in the Gromacs-ligand tutorial 
> available
> on the PRODRG FAQ page
>
> Daan
>
> On Tue, 5 Oct 2004, Yunfeng Hu wrote:
>
>> Hi, I used prodrg to obtain a topology file for the ligand and
>> generated the complex topology file of a enzyme-ligand complex after
>> modifying the enzyme topology file. After adding water box, grompp
>> complains about atomtype OS not found which seems strange. I have 
>> found
>> a similar discussion in the mailing-list before and no final solution
>> was offered. Here are the commands I used:
>>
>> pdb2gmx -merge -f complex.pdb -p complex.top -o complex.gro
>> editconf -bt cubic -f complex.gro -o complex_h2o.gro -c -d 0.85
>> genbox -cp complex_h2o.gro -cs spc216.gro -o complex_b4em.gro -p
>> complex.top
>> grompp -f em.mdp -c complex_b4em.gro -p complex.top -o complex_em.tpr
>> ...
>> creating statusfile for 1 node...
>>
>> checking input for internal consistency...
>> calling /usr/bin/cpp...
>> processing topology...
>> Generated 279 of the 1225 non-bonded parameter combinations
>> Cleaning up temporary file grompptjdQeY
>> Fatal error: Atomtype 'OS' not found!
>>
>>
>> Thank you for any suggestions.
>>
>> -Eric
>>
>> _______________________________________________
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>
>
###################################
Yunfeng Hu, Ph.D
Research Associate
Department of Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037
Tel. (858) 784-2204
Fax. (858) 784-2860
Emal: yunfeng at scripps.edu
Web: http://www.scripps.edu/~yunfeng
###################################