The error message already tells you what is going wrong:
Invalid order for directive atomtypes, file 
""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1

so what is the first line from /usr/local/gromacs/share/gromacs/top/chcl3.itp ?
It's [ atomtypes ]
This is a parameter definition and should come before topology definition. Therefore move this section to come right after you include ffoplsaa.itp


###############################

; Include water topology
#include "chcl3.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
  1    1       1000       1000       1000
#endif

###############################

I further note that you have not included any CCl3 molecules in your topology, 
you should do this:


[ molecules ]
; Compound        #mols
Protein             1
CCl3             512 ;; or whatever your number is

##############################

Obviously I have not touched on residue 'FEN', a nonstandard oplsaa residue 
that I know nothing about.

Why did pdb2gmx not generate a topology that was error-free? Because it (and 
other tools such as genbox, genion)
are designed for proteins in water with ions. Anything non-standard is going to 
require an enhanced understanding of
input files and I therefore suggest that you read the topology section of the manual much more closely before proceeding. You would have found your answer on pg 98 and 109 of the gromacs-3.3 manual.

Chris.

---original message---
Hi all,
I'm trying to run a simulation of a phenol in chloroform with the oplsaa 
forcefield.
I've downloaded the chloroform box from gromacs and added the files to the top 
folder.
Everything is fine till I run grompp which says:

Fatal error:
Invalid order for directive atomtypes, file 
""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1


After downloading the chcl3 box should i have to modify something else?
I've checked in the manual but I'm not able to understand what i'm doing wrong.

This is the top file of my phenol I get after running pdb2gmx:

;
;       File 'fenolo.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Fri Jan 25 15:47:30 2008
;
;       This is your topology file
;       "Ramones For Ever" (P.J. Van Maaren)
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    
chargeB      massB
    1   opls_145      1    FEN     CG      1     -0.193     12.011   ; qtot 
-0.193
    2   opls_145      1    FEN    CD2      2    -0.1642     12.011   ; qtot 
-0.3572
    3   opls_145      1    FEN    CE2      3    -0.3176     12.011   ; qtot 
-0.6748
    4   opls_166      1    FEN     CZ      4     0.5484     12.011   ; qtot 
-0.1264
    5   opls_145      1    FEN    CE1      5    -0.3953     12.011   ; qtot 
-0.5217
    6   opls_145      1    FEN    CD1      6    -0.0852     12.011   ; qtot 
-0.6069
    7   opls_146      1    FEN    HD2      7      0.171      1.008   ; qtot 
-0.4359
    8   opls_146      1    FEN    HE1      8      0.163      1.008   ; qtot 
-0.2729
    9   opls_146      1    FEN    HE2      9     0.1907      1.008   ; qtot 
-0.0822
   10   opls_146      1    FEN    HD1     10     0.1506      1.008   ; qtot 
0.0684
   11   opls_146      1    FEN     HG     11     0.1496      1.008   ; qtot 
0.218
   12   opls_167      1    FEN     OH     12    -0.6515    15.9994   ; qtot 
-0.4335
   13   opls_168      1    FEN     HH     13     0.4334      1.008   ; qtot 
-0.0001

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
1 2 1 1 6 1 1 11 1 2 3 1 2 7 1 3 4 1 3 9 1 4 5 1 4 12 1 5 6 1 5 8 1 6 10 1 12 13 1
[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
1 4 1 1 8 1 1 9 1 2 5 1 2 10 1 2 12 1 3 6 1 3 8 1 3 11 1 3 13 1 4 7 1 4 10 1 5 9 1 5 11 1 5 13 1 6 7 1 6 12 1 7 9 1 7 11 1 8 10 1 8 12 1 9 12 1 10 11 1
[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
2 1 6 1 2 1 11 1 6 1 11 1 1 2 3 1 1 2 7 1 3 2 7 1 2 3 4 1 2 3 9 1 4 3 9 1 3 4 5 1 3 4 12 1 5 4 12 1 4 5 6 1 4 5 8 1 6 5 8 1 1 6 5 1 1 6 10 1 5 6 10 1 4 12 13 1
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2         
   c3            c4            c5
6 1 2 3 3 6 1 2 7 3 11 1 2 3 3 11 1 2 7 3 2 1 6 5 3 2 1 6 10 3 11 1 6 5 3 11 1 6 10 3 1 2 3 4 3 1 2 3 9 3 7 2 3 4 3 7 2 3 9 3 2 3 4 5 3 2 3 4 12 3 9 3 4 5 3 9 3 4 12 3 3 4 5 6 3 3 4 5 8 3 12 4 5 6 3 12 4 5 8 3 3 4 12 13 3 5 4 12 13 3 4 5 6 1 3 4 5 6 10 3 8 5 6 1 3 8 5 6 10 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "chcl3.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
fenolo in chcl3

[ molecules ]
; Compound        #mols
Protein             1


Thanks in advance

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