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

[Jignesh Patel]

Dear Mark,

I have used following .top file.

; Include forcefield parameters
#include "ffG53a6.itp"
#include "drg.itp"

[ 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
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