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) ?
#2
Before I started to search how in leap this bond limitation is implemented
of course
that I searched mailing list.
Practically I found out just one type of suggestion which is perhaps
connected with
leap sentence "-- setting atoms pert=true override default limits"
generated as a part
of "Bond: Maximum coordination exceeded" error. (but not sure that it was
useful to all
perhaps because the usage was not explained fully)
I have tried with the syntax found in contributions like this:
http://archive.ambermd.org/201008/0660.html
e.g.
set UNIT_NAME.RES_NUMBER.ATOM_NAME pert true (1)
and then I tried to add missing bonds using "bond" command.
But (1) just did something like deleting of the ATOM_NAME atomtype
so I got problem with suddenly undefined parameters like
- c3
-c3-3 etc.
however after "desc ATOM_NAME" listed that the atom type of ATOM_NAME is OK
and of course all the necessary parameters was already loaded using FRCMOD
file.
This problem I fixed by adding another set commands which I found in
mailing list.
set UNIT_NAME.RES_NUMBER.ATOM_NAME pert true
set UNIT_NAME.RES_NUMBER.ATOM_NAME pertName ATOM_NAME
set UNIT_NAME.RES_NUMBER.ATOM_NAME pertType ATOM_NAME_TYPE
Then problem with undefined parameters (which of course was defined and
loaded in FRCMOD file)
disappeared but I was still not able to save my residuum with all desired
bonds.
Later I found this "pert" keyword in connection with TI
see here:
http://archive.ambermd.org/200701/0413.html
http://archive.ambermd.org/200607/0332.html
so I am a bit confused as it seems to me that with pert true one can do
something like to label
atom/s which will be perturbed (decoupled from the system) during TI or
something like that ?
I already did some TI calc. never used such key words like "pert true" and
in AmberTools manual I found practically nothing about this keyword, Is
there any relevant documentation available ?
So please can you put some light here and explain
a)
what is the true/original purpose of "pert true" keyword ?
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).
There is perhaps some connection as it is clear from mailing list but
also from the leap sentence "-- setting atoms pert=true override default
limits",
but perhaps it is not fully clear what this sentence really tels e.g.
how exactly to use "pert true" keywords or which another "set" commands
have to be applied to allow for the atom X in my residuum more than
default max. number of bonds. and successful saving of PRMTOP and INPCRD
files
with all desired bonds.
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 ?
#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.
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 ?
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 ?
Thank you very much in advance for your explanations !
Best wishes,
Marek
Dne Sun, 24 Feb 2013 16:22:22 +0100 David A Case
<case.biomaps.rutgers.edu> napsal/-a:
> On Sun, Feb 24, 2013, Marek Maly wrote:
>>
>> I would like to know if it is possible to change the default Antechamber
>> limit of 6 bonded atoms
>> (to the given atom) e.g. by increasing value of some "MaxBonds"
>> parameter
>> from default 6 to desired number in some antechamber source file (and
>> recompiling) or for the moment this limitation is absolute
>> i.e. no way to increase limitation of 6 bonded atoms ?
>
> Antechamber deals with a (large) subset of "organic molecules"; it
> doesn't
> know about any atom types that would be bonded to more than 6 other
> atoms.
> I'm guessing that not only the input files (in
> $AMBERHOME/dat/antechamber) but
> also the internal logic of the chemical similarity routines would need
> to be
> changed to accommodate what is really a different class of molecule.
>
> So I think the short answer is "no".
>
> ....dac
>
>
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Received on Mon Feb 25 2013 - 17:00:02 PST
