[gmx-users] About "Invalid order for directive atomtypes"
Alan
alanwilter at gmail.com
Wed Jul 16 19:35:25 CEST 2008
Hi Hans,
Bottom line, when faced this problem, is:
>>>>> #include "ffamber03.itp"
>>>>> ; Include chain topologies
>>>>> #include "topol_A.itp"
>>>>> #include "topol_B.itp"
>>>>> #include "topol_FAD.itp"
>>>>> #include "topol_ZTRP.itp"
Always put your ligand itp right after #include "ffamber03.itp" (or
whatever forcefield), i.e, never after chains topologies.
This always worked for me. But you have a point, from the manual I was
expecting it to work no matter the order. Bug?
Cheers,
Alan
On Wed, Jul 16, 2008 at 6:16 PM, <gmx-users-request at gromacs.org> wrote:
> ------------------------------
>
> Message: 4
> Date: Wed, 16 Jul 2008 18:06:20 +0100
> From: Hans Martin Senn <senn at chem.gla.ac.uk>
> Subject: Re: [gmx-users] About "Invalid order for directive atomtypes"
> error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <91A2AB63-73BD-4614-871E-F4DA53736AB5 at chem.gla.ac.uk>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> 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
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 16 Jul 2008 20:13:46 +0300
> From: "Vitaly Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] RE: Gromacs and restraints
> To: gmx-users at gromacs.org
> Message-ID:
> <7138ee40807161013s21a64933o390e6bfb236f56b0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
>>I will be running protein in explicit water simulations and need a timestep
>>of 2fs. Forces and energies in the system will be analyzed. What restraint
>>setup should I choose?
>
> I think no critical errors would occur if you use shake or lincs for
> water in your case.
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 16 Jul 2008 20:09:35 +0300
> From: "Vitaly Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] RE: Using user-tables for simulations in vacuum
> To: gmx-users at gromacs.org
> Message-ID:
> <7138ee40807161009j6dae425bw2b0ea5a7a163bea9 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
>>There is no error message except for "segmentation fault". It does the
>>same thing if I try to energy minimize the system instead of running an MD
>>simulation. The corresponding mdp file is pasted below:
>
> Try to make emstep lower. Check your constraints. Check the potential
> and its details.
>
> When segmentation fault occurs, it often means that something is wrong
> with your configuration.
>
> Best,
> Vitaly
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 51, Issue 65
> *****************************************
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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