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

[Xavier Periole]

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
> 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

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