[gmx-users] Re: Regarding Error "Atom type OS not found"

[Justin A. Lemkul]

Jignesh Patel wrote:
> Dear Mark,
> 
> I have used following .top file.
> 
> ; Include forcefield parameters
> #include "ffG53a6.itp"
> #include "drg.itp"

Let me guess, drg.itp is from PRODRG?  Then you probably have ffgmx atom types 
(like "OS") that are not supported by G53a6.  Thus you are mixing force fields 
and generating an inconsistent physical model.  There is PRODRG beta (2.5) that 
generates G96-compatible topologies, but the usual caveats about their accuracy 
apply :)

-Justin

> 
> [ moleculetype ]
> ; Name            nrexcl
> Protein_X           3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1         NL      1    SER      N      1      0.129    14.0067   ; 
> qtot 0.129
>      2          H      1    SER     H1      1      0.248      1.008   ; 
> qtot 0.377
> ------
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
> 
> ;Include ligand topology
> ;#include "drg.itp"
> 
> 
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound        #mols
> Protein_X           1
> yoh                    1
> 
> Thanking you in anticipation.
> 
> 
> On 13/04/2010 1:49 PM, Jignesh Patel wrote:
>  > Hello,
>  >
>  > while I am running grompp command, I am getting following error.
>  >
>  > Opening library file /usr/local/gromacs/share/
> gromacs/top/ff_dum.itp
>  > Generated 837 of the 2346 non-bonded parameter combinations
>  > -------------------------------------------------------
>  > Program grompp, VERSION 4.0.5
>  > Source code file: toppush.c, line: 947
>  > Fatal error:
>  > Atomtype OS not found
>  >
>  > Can anyone help me to solve this problem?
> 
> Yep, they can point out that atom type OS is not found. Since at this
> stage only you know about your topology and system preparation, and more
> particularly why you're trying to #include "ff_dum.itp", only you can
> reason why. Perhaps sharing some more detail will help...
> 
> Mark
> 
> 
> -- 
> Best Wishes,
> Jignesh Patel
> Pharmacoinformatics,
> NIPER
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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