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 list-improper-per-residue is superseded by the current FF.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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 27 2013 - 11:30:03 PST
