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list-improper-per-residue is superseded by the current FF.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 ?
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 ?
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 ?
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 ?
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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Received on Wed Feb 27 2013 - 10:30:03 PST
