Nilesh Dhumal wrote:
Thanks Justin,
Here I pasted water.top
;
; File 'water.top' was generated
; By user: ndhumal (36026)
; On host: c63
; At date: Thu Apr 21 14:52:38 2011
;
; This is your topology file
; Protein
;
; Include forcefield parameters
#include "ffoplsaa.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"
Up to this point, you haven't defined any molecules. You've commented out every
topology and applied a [position_restraints] directive to a non-existent
moleculetype. So you've defined a force field, and then a system for which no
molecules exist, hence the error.
-Justin
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
SOL 256
Nilesh
On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation for flexiable water. I use the
parameters from J. Chem. Phys. (2006),124,024503 paper and made a
spc_fw.itp file.
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_116 OW 8 9.95140 -0.820 A 3.165492e-01
6.50299455e-01
opls_117 HW 1 4.03200 0.410 A 0.00000e+00
0.00000e+00
[ bondtypes ]
; i j func b0 kb
OW HW 1 1.012 443153.3808 ; J. Chem. Phys.
(2006),124,024503
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 113.24 317.5656 ; J. Chem. Phys.
(2006),124,024503
I am geting the error for
grompp -f minim.mdp -c water.pdb -p water.top -o 1.tpr
error I am getting
rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415
Fatal error:
Syntax error - File water.top, line 26
Last line read:
'[ system ]'
Invalid order for directive system
How can I fix this error?
Assemble the components of your .top in the correct order, as described
in chapter 5 of the manual. Without seeing the contents of "water.top"
that's the best anyone can offer.
-Justin
Nilesh
--
========================================
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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--
========================================
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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