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

[Xavier Periole]

On Wed, 16 Jul 2008 17:24:22 +0100
  Hans Martin Senn <senn at chem.gla.ac.uk> wrote:
> Hi Xavier
> 
> On 16 Jul 2008, at 15:51, Xavier Periole wrote:
>> On Wed, 16 Jul 2008 15:04:17 +0100
>> Hans Martin Senn <senn at chem.gla.ac.uk> wrote:
>>> 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.
>> It might be that the same protein name is in two of your different
>> topology files.
>> The problem is certainly somewhere in those topologies.
> 
> By "protein name", do you mean the [ moleculetype ] section? If so,  the 
>answer is no. Each of the molecule itp files specifies exactly one  molecule 
>type (protein chain or ligand); the names are unique.
> Of course it is fair to say that the problem is in the topologies, as 
> demonstrated by my solution to the problem... The point is that it is 
> apparently not permitted to have [ atomtypes ] (in topol_FAD.itp)  after 
>having read other molecule definitions (in topol_{A,B}.itp), in  contrast to 
>what I think the manual suggests.
Then you got a solution!? Great!
I actually do not know if atomtypes can be after moleculetypes. But you
could try to include the topol_TAD.itp first, or put the atomtypes with
the other ones. If you actually need a solution.
XAvier
> Hans
> 
> 
> 
>>> 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
> 
> 
> 
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-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------