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

[Justin A. Lemkul]

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

> 
> Cheers
> Hans
> 
>> 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
> 
> .......................................................
> 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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-- 
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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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