[gmx-users] About "Invalid order for directive atomtypes" error
Xavier Periole
X.Periole at rug.nl
Wed Jul 16 16:51:07 CEST 2008
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.
>
>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
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