"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 list-improper-per-residue is superseded by the current FF.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 ?
Leap matches impropers by atom types and topology, not by the
old IMPROPER section.
>
> 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 ?
Add to the improper section of frcmod. Note the improper will match
all instances of atom types + topology.
>
> But there might be also the possibility that in the given group of atoms
> where I would like to maintain e.g. planarity is/are also NEW (by me
> defined atom type/s)
> atom types. Is at least in this case the improper info in IMPROPER record
> of prepin file
> accepted by leap or it is still ignored ? If it is ignored the question is
> the same
> like above, where to put the information/definition of the improper
> torsions which leap
> would not add by default ?
Same answer as above.
>
> If the IMPROPER records are accepted by leap at least in the situation when
> there are new atom types we are OK here in the situation of using PREPIN
> file
> but what in the same situation when using MOL2 instead PREPIN ?
The IMPROPER section in prep.in is only used for debug purposes.
It has no effect on the impropers that are used in the parm file.
Bill
> 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).
>
> Thanks again !
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
>
> Dne Tue, 26 Feb 2013 02:19:17 +0100 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > On Mon, Feb 25, 2013 at 7:31 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> >
> >> Dear prof. Case,
> >>
> >> first of all thank you very much for your comments !
> >>
> >> Meanwhile I did some progress. I found out that the solution how to
> >> prepare/parametrize molecular residuum/molecule which is problematic for
> >> Antechamber
> >> due to the unusually high number of bonds (for Antechamber higher than
> >> 6)
> >> might be to use of MOL2+FRCMOD (where Antechamber is not necessary)
> >> instead of
> >> PREPIN+FRCMOD (where Antechamber is involved).
> >>
> >> If one use MOL2 + FRCMOD there is necessary to solve similar problem as
> >> in
> >> case
> >> of Antechamber but now just with tleap and as I found the solution is
> >> probably
> >> very simple at the end.
> >>
> >> It seems (at least in case of Amber12) that only adjusting of MAXBONDS
> >> symbolic constant (with the actual value 8) in
> >> AmberTools/src/leap/src/leap/atom.h and recompiling is enough.
> >>
> >> prmtop + inpcrd files created successfully, pmemd.cuda seems to have
> >> also
> >> no problems
> >> with my residuum containing 12 coordination bonds to one atom.
> >>
> >> But I have some related additional questions:
> >>
> >> #1
> >> Is this approach really OK (secure) ?
> >>
> >
> > I'm not sure. You could always check that the parameters you expect to
> > see
> > in the topology file are really there. ParmEd and rdparm can help with
> > this.
> >
> > You are probably one of a very (very) small number of people attempting
> > more than 6 bonded partners to a single atom, so you're unlikely to get
> > any
> > definitive answers. At the very least, you will need to validate your
> > model.
> >
> >
> >> #2
> >> Before I started to search how in leap this bond limitation is
> >> implemented
> >> of course
> >> that I searched mailing list.
> >>
> >> [snip]
> >> So please can you put some light here and explain
> >>
> >> a)
> >> what is the true/original purpose of "pert true" keyword ?
> >>
> >
> > This is very old (in Amber-years) and is now deprecated. This was
> > originally used by the "Gibbs" program, which stopped being released well
> > before I joined the project. [1] In the past, TI was performed by
> > specifying a 'perturbed' residue in the topology file. Basically, the
> > prmtop stored information about both end states (lambda = 1 and lambda =
> > 0). The parts that differed between the two end states had both sets of
> > parameters present.
> >
> > b)
> >> how is "pert true" related to the problem of leap acceptance
> >> of more bonds to the given atom than is the actual max. default (defined
> >> in atom.h).
> >>
> >
> > Since both endpoints are present in the topology file, tleap has to
> > support
> > an atom being bonded to different atoms in each state. Therefore, one
> > atom
> > _could_ be bonded to 4 atoms in the lambda=0 state, and all 4 of those
> > atoms could change in the lambda=1 state. Therefore, that one atom needs
> > to `bond' to 8 atoms (although not more than 4 atoms would be `active' at
> > any given value of lambda).
> >
> > What I'm not sure about is whether setting "pert" to `true' simply
> > bypasses
> > the atom bond limits or whether it does something else, too. Since no
> > extra sections of the prmtop are printed out, I suspect it just ignores
> > the
> > hard-coded atom limits, but you should verify this (again, with ParmEd or
> > something similar).
> >
> > [snip]
> >>
> >> c)
> >> If "pert true" can really solve the bond problem, is this way more
> >> appropriate/recommended
> >> or it is just equivalent to simple redefinition of MAXBONDS constant in
> >> atom.h ?
> >>
> >
> > I'm not sure. I suspect they're equivalent in this particular instance,
> > but again this is a highly atypical application.
> >
> >
> >>
> >> #3
> >> Regarding substitution of PREPIN file by MOL2 file:
> >>
> >> There are some information in PREPIN file which
> >> are not (at least by default) present in MOL2 like
> >>
> >> a)
> >> IMPROPER record
> >> which defines groups of atoms (using atom names) for which improper
> >> torsions have to be used (e.g. aromatic rings).
> >>
> >> How to incorporate this important information into MOL2 file ?
> >> I checked MOL2 format ( http://www.tripos.com/data/support/mol2.pdf )
> >> and did not found any IMPROPER section.
> >>
> >
> > This information should not need to be present --- tleap should
> > automatically apply known improper torsions that it recognizes.
> >
> > b)
> >> In PREPIN file there is also section LOOP where all
> >> the loops are defined but this info is sufficiently
> >> substituted in MOL2 file by the complete list of all
> >> bonds I guess. Am I right ?
> >>
> >
> > I don't know what the LOOP section does.
> >
> > c)
> >> There are also 3 DU atoms in the start
> >> of the atom list in PREPIN file defining
> >> cartesian system. Are these DU atoms
> >> necessary also in case of MOL2 definition
> >> of the given residuum /molecule? If yes how to define
> >> them ?
> >>
> >
> > DU atoms are only necessary because the PREPIN uses internal coordinates
> > (that is the IN part of prepin -- prepc or prepcar files use cartesian
> > coordinates). The dummy atoms are necessary to uniquely define the
> > position of the first, second, and third atoms. [2]
> >
> >
> > 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).
> >
> > References:
> > [1]: <hearsay>It had some clever code that was able to efficiently
> > calculate TIs by only calculating the pairwise differences. However, it
> > was not well-parallelized, and when pairwise-decomposable methods
> > (cutoffs,
> > distance-dependent dielectric) began to be replaced by non-pairwise
> > decomposable methods (Ewald, GB, PB), this approach was no longer
> > rigorously correct. Therefore, TI was implemented using a dual-topology
> > approach in sander and Gibbs was dropped. </hearsay>
> >
> > [2] I suspect this is really just an implementation detail. Since the
> > positions of DU are arbitrary, so is the position of the first 3 atoms,
> > technically---at least in Cartesian space. Adding 3 dummy atoms does
> > allow
> > the first atom's position to be specified by a distance, angle, and
> > dihedral, just like every other atom.
> >
> > HTH,
> > Jason
> >
>
>
> --
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>
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Received on Wed Feb 27 2013 - 11:30:04 PST
