[gmx-users] About "Invalid order for directive atomtypes" error
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 16 18:50:12 CEST 2008
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.
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
>
> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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