[gmx-users] Overriding Wildcard dihedraltypes

hubert santuz hubert.santuz at gmail.com
Thu Jan 9 19:15:15 CET 2014

I tried your second procedure and it works as well.
I prefer this one, it's a more movable way ;)

Le 09/01/2014 18:29, Mark Abraham a écrit :
> On Thu, Jan 9, 2014 at 5:51 PM, hubert santuz <hubert.santuz at gmail.com>wrote:
>> Hi,
>> First, thanks for your detailed response.
>>   Thanks for the question, and particularly the detail. It seems that you
>>> are
>>> trying use a [dihedraltypes] section in my_molecule.itp, which is
>>> generally
>>> a bad idea, because all such directives must appear before the first
>>> [molecule] directive, which defeats the point of molecule.itp files being
>>> somewhat movable. Because of that intention for molecule.itp files,
>>> there'd
>>> be no reason to have separate [dihedraltypes] sections that should be
>>> logically treated together, so the code assumes such sections are
>>> separable, and so you get unintended behaviour (perhaps particularly with
>>> wildcard atom types, and/or type 9 dihedrals) unless you change
>>> ffbonded.itp like you have now done.
>> By trying to simplify my problem, I have misleading you.
>> In fact, I have 2 itp files for my molecule (its is the cholesterol) :
>>    - One containing all the *types sections [atomtypes, bondtypes,
>> dihedraltypes] (params_chol.itp)
>>   - The second one is a 'regular' itp file containing [molecules, atoms,
>> bond ] sections. (cholesterol.itp)
>> So, in my topol. top, I have in reality this :
>> #include "charmm36.ff/forcefield.itp"
>> #include "params_chol.itp"
>> #include "cholesterol.itp"
>> My [dihedraltypes] directive is then before the [molecule] directive.
>> I have to do this because I have 2 new atoms for this molecule so I need
>> to declare them somewhere. Therefore, I also need to declare the bondtypes,
>> angletypes and dihedraltypes associated with these 2 new atoms.
>> All is working well except this dihedral override.
>> That's why I suspected a bug but maybe it is that part I'm not doing in
>> the good way...
> Yes, the above is more workable, but it has the same problem that
> cholesterol.itp depends on correctly formed [dihedraltypes]. I think it is
> likely that the implementation assumes you would not try to declare a set
> of additive [dihedraltypes] in such a modular way, since the
> copy-and-modify-ffbonded.itp procedure is available. Not ideal, but odds
> are excellent it won't be fixed, either ;-)
Yes I understand but overriding an explicit dihedraltypes is working ;)
But anyway, I found a solution.

Thanks for your detailed explanations.


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