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

[Alan]

Justin and Hans,

So, as far as I could find, any itp containing [ atomtypes ] has to
come first. However, I never dealt with more than one ligand topology
itp file.

Besides, from the manual, I was expecting that even having others [
atomtypes ] declared in others itp files the last atomtype read (case
of double definition) would be taken. If it doesn't work this way,
despite Justin explanation, why not do it?

Moreover, what Justin said I would totally agree if in ligand [
atomtypes ] I was redefining atomtypes already done by ffamber*.itp,
but I use gaff too and its atomtypes (lower case) are definitely not
called before than in the ligand itp file. So here's where I found the
manual not clear.

Cheers,
Alan

> Message: 4
> Date: Wed, 16 Jul 2008 19:57:33 +0100
> From: Hans Martin Senn <senn at chem.gla.ac.uk>
> Subject: Re: [gmx-users] About "Invalid order for directive atomtypes"
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Alan <alanwilter at gmail.com>
> Message-ID: <A77FD839-29FA-4DB2-912A-91A6FC82ABDE at chem.gla.ac.uk>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi Alan
>
> On 16 Jul 2008, at 18:35, Alan wrote:
>> 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.
>
> Just to clarify: This works only if topol_FAD.itp (the only one
> containing [ atomtypes ]) goes first! It fails if any molecule itp
> (protein chain OR other ligand) is included before.
>
> Cheers
> Hans

> ------------------------------
>
> Message: 5
> Date: Wed, 16 Jul 2008 15:08:24 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] About "Invalid order for directive atomtypes"
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <487E4728.5000205 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Hans Martin Senn wrote:
>> Hi Alan
>>
>> On 16 Jul 2008, at 18:35, Alan wrote:
>>> 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.
>>
>> Just to clarify: This works only if topol_FAD.itp (the only one
>> containing [ atomtypes ]) goes first! It fails if any molecule itp
>> (protein chain OR other ligand) is included before.
>
> Probably because other parameters are dependent upon these atomtypes.  Including
> new atomtypes after the specification of, for example, pairs and other
> non-bonded interactions might not give the desired result.  That is, grompp
> needs to know beforehand the types of interactions between FAD and the
> protein(s), instead of trying to backtrack when it encounters new atomtypes.
> According to the manual (p. 109, which I agree probably needs a small tweak),
> "After the definition of new atom type(s), additional non-bonded and pair
> parameters can be defined."  Key word is "after," so new atomtypes always need
> to follow the force field definition, but can be in multiple sections and will
> not over-write previous entries.
>
> -Justin
>


-- 
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<<