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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