[gmx-users] About "Invalid order for directive atomtypes" error

[Hans Martin Senn]

Dear all

This is a topic that has come up a couple of times here, see, e.g., http://www.gromacs.org/pipermail/gmx-users/2008-January/032114.html 
.
However, despite the recommendations given in that previous post, I  
think the problem is exactly that the information in the manual is not  
sufficiently accurate or clear in this case.

Specifically: I have a protein with two bound ligands, ZTRP and FAD.
- For the protein I use ffamber03. pdb2gmx created two itp files for  
the two chains.
- For ZTRP, I have built an itp file using AMBER atom types (as  
defined in ffamber03.atp or ffamber03nb.itp).
- For FAD, I have an itp file generated using antechamber and amb2gmx.  
It contains an [ atomtypes ] section defining the GAFF atom types.

This was my first go at assembling it all in the top file:

 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
; Include forcefield parameters
#include "ffamber03.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_FAD.itp"
#include "topol_ZTRP.itp"

; Include water topology
#include "ffamber_tip3p.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Full system in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
ZTRP                  1
FAD                   1
SOL             20893
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

However, grompp complained about "Invalid order for directive  
atomtypes" when including topol_FAD.itp.

Following a hint from the mailing list, I took the [ atomtypes ]  
section out of topol_FAD.itp and put it into a separate itp file "GAFF- 
types.itp", which is included before the other molecule itp files. The  
final top file then looked like this:

 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
; Include forcefield parameters
#include "ffamber03.itp"

; Define GAFF atomtypes here (not in molecule itp file) to avoid  
'Invalid order' error
#include "GAFF-types.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_FAD.itp"
#include "topol_ZTRP.itp"

; Include water topology
#include "ffamber_tip3p.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Full system in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
ZTRP                  1
FAD                   1
SOL             20893
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

This solved the problem. However, and this is my main point here, the  
manual for GROMACS 3.3, p. 98 says:
"starting with GROMACS version 3.1.3 all directives at the parameter  
level can be used multiple times and there are no restrictions on the  
order..."

In my reading, this means that [ atomtypes ] can be defined anywhere  
(as long as it is before they are referred to for the first time),  
which is clearly at variance with the observed behaviour. Am I  
misinterpreting it, or is the manual not precise enough here?

A final note: Since simulating a protein with bound ligands is an  
extremely common case and since this issue about "Invalid order" seems  
to come up regularly, it would be very helpful if a corresponding  
HOWTO was available in the manual/FAQ/wiki to settle it once and for  
all.


Best wishes
Hans



.......................................................
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow

E-mail: senn at chem.gla.ac.uk
Direct line: +44 (0)141 330 6574
Fax: +44 (0)141 330 4888

Department of Chemistry
Joseph Black Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK