[gmx-users] grompp error
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 22 02:03:01 CEST 2011
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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