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

[Hans Martin Senn]

Hi Justin

On 16 Jul 2008, at 17:50, Justin A. Lemkul wrote:
> Hans Martin Senn 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.
>
> Just thinking out loud, and this may or may not do anything, but I  
> know that a lot of problems encountered involving topologies result  
> from having things in the wrong order.  For example, you've included  
> the FAD.itp before ZTRP.itp, but then called ZTRP before FAD in the  
> [ molecules ] section.  I know things in the [ molecules ] section  
> need to line up with what's in the .gro/.pdb file, but I don't know  
> about for certain about order within the topology.  I once included  
> a ligand topology after the water #include statement by mistake, and  
> got a different error, but fixing the order solved everything.
>
> Try switching the respective molecule definition or .itp call to  
> correspond to whatever is in your structure file, and see if that  
> does anything.

It does not (I should have said that I tried that). As you point out,  
the order in which the components are listed in the [ molecules ]  
section DOES matter. However, it seems that the corresponding itp  
files can be included in a different (arbitrary?) order.


Cheers
Hans


> Again, this may or may not be worth anything, but it's something I'd  
> try if all else leaves me scratching my head :-)
>
> -Justin


>>>> 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