Dear Jason and Bill,
yes it is clear, sorry for my greenhorn question
regarding impropers, I was just a confused a bit
by the fact that in PREPIN the impropers are definded by
the atom name, but it is clear that important have to be just
more general atom-type based definitions in ff or frcmod file like in
case of any other parameter. Thanks also for the answer regarding
HAD/TAIL atoms.
Best wishes,
Marek
Dne Wed, 27 Feb 2013 20:12:43 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> On Wed, Feb 27, 2013 at 1:03 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Dear Jason and Bill,
>>
>> first of all thanks a lot for your
>> useful comments !
>>
>> I have just the last two questions regarding your comments:
>>
>> A) IMPROPER RECORD
>>
>> YOUR COMMENTS
>> --------------------------------------------------------------------
>> JASON
>> This information should not need to be present --- tleap should
>> automatically apply known improper torsions that it recognizes.
>>
>> BILL
>> If it is added to a prep.in file (instead of a mol2) the list will
>> be checked against the impropers the FF assigns. This can be useful
>> for developing improper torsions. But for practical purposes the
>> list-improper-per-residue is superseded by the current FF.
>> ---------------------------------------------------------------------
>>
>> So if I understood well the IMPROPER record has rather informative
>> character
>> in case that one is using just Amber-known atom types, these information
>> are rather ignored and leap will "decide" automatically where to add
>> impropers
>> am I right ?
>>
>
> Yes, I believe you are right. tleap will decide where to add impropers
> based on what impropers are defined in the force field (parm.dat,
> frcmods,
> etc.). (Someone will correct me here if I'm wrong)
>
>
>>
>> So if one would like to add some improper torsion to group of 4 atoms
>> with known Amber atom types, the IMPROPER record in prepin file is
>> definitely not the right place. Am I right ? So how can one solve
>> this eventual problem i.e. where one can define these impropers in way
>> that they are not ignored by leap ?
>>
>
> frcmod file.
>
>
>> YOUR COMMENT
>>
>> -----------------------------------------------------------------------------
>> Ultimately, there is only one thing that the prepin file has that the
>> mol2
>> file does not --- connection information. The prepin file allows you to
>> specify a head and tail atom so that tleap will automatically chain it
>> to
>> adjacent residues. You can set those atoms by hand, though, and the
>> q4md
>> folks modified the mol2 file to add this data (see the mol3
>> documentation
>> on their website, which is supported in AmberTools 12).
>>
>> --------------------------------------------------------------------------------
>>
>> So if I use MOL2 file just as the container for individual residues
>> (instead of PREPIN)
>> (not as the container for the whole molecule) I will need to define HEAD
>> and the TAIL atom to successfully connect adjacent residues in e.g. PDB
>> file with the whole molecular structure.
>>
>> But in my opinion if e.g. in PDB file with the whole molecular structure
>> is also sufficient
>> connectivity information - at least that regarding connectivity of the
>> "border" residues
>> atoms, there is perhaps no need to maintain in residue file info. which
>> atoms are the
>> border ones (HEAD and TAIL).
>>
>
> If the PDB file has CONECT records that are correct (and you haven't
> deleted atoms to make the atom indexes incorrect), then I think tleap
> will
> add the bonds correctly. If the CONECT records are not present, you will
> either have to set the HEAD/TAIL or add the bonds manually.
>
> HTH,
> Jason
>
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Received on Wed Feb 27 2013 - 12:00:03 PST
