leila karami wrote:
dear justin
Fatal error:
[ file spc.itp, line 46 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
I checked topology file and sent topology and spc.itp file. please guide me.
this is my topology file :
; Include forcefield parameters
#include "ffamber03.itp"
; Include chain topologies
#include "c_A.itp"
#include "c_B.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 in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7127
this is my spc.itp file:
Note how that in spc.itp, none of the #ifdef statements cover any of the AMBER
force fields. You must either create the appropriate entry, or use a water
model that is, by default, compatible with AMBER.
-Justin
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifdef _FF_GROMACS
1 OW 1 SOL OW 1 -0.82
2 HW 1 SOL HW1 1 0.41
3 HW 1 SOL HW2 1 0.41
#endif
#ifdef _FF_GROMOS96
#ifdef HEAVY_H
1 OW 1 SOL OW 1 -0.82 9.95140
2 H 1 SOL HW1 1 0.41 4.03200
3 H 1 SOL HW2 1 0.41 4.03200
#else
1 OW 1 SOL OW 1 -0.82 15.99940
2 H 1 SOL HW1 1 0.41 1.00800
3 H 1 SOL HW2 1 0.41 1.00800
#endif
#endif
#ifdef _FF_OPLS
1 opls_116 1 SOL OW 1 -0.82
2 opls_117 1 SOL HW1 1 0.41
3 opls_117 1 SOL HW2 1 0.41
#endif
#ifdef _FF_CHARMM
1 OW 1 SOL OW 1 -0.82
2 HW 1 SOL HW1 1 0.41
3 HW 1 SOL HW2 1 0.41
#endif
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#else
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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