Thanks Jonathan, that is exactly the problem. In the moment that I fist
work with this enzyme, a few years back, I used the parameters for ATP from
the same source. Lately I was considering to change that because I observed
that the parameters do not work fine in MM simulations (some O-P distances
are too short), but as this problems do not show under QM/MM I been
postponing the change for later. So, back to topic, I checked the topology
file and found under the flag of the atomic number, the three conflictive O
atoms have a charge of -1. A simple editing of the topology file changing
-1 with 8, is enough to get the calculation running with AmberTools15.
Thanks Jonathan and Gustavo for your help in solving the mystery of the
^.^. atoms.
2015-10-05 22:17 GMT+02:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
> OK, that helps *a lot*. There has been a pretty expense discussion on a
> related issue on the Amber list:
>
> http://archive.ambermd.org/201110/0035.html
>
> The problem seems to be the following:
>
> in the past (probably when those files were created) the atomic numbers
> weren’t used for anything in Amber. For some reason, the creator of the
> files left negative atomic numbers there. I suppose it had some other
> meaning for him.
>
> Now we come to the present, and Amber now has the atomic numbers in the
> prmtop file, and DFTB and other routines that need the atomic numbers get
> them from it. However, when the promote file was created using these old
> prep files, the atomic numbers may come negative.
>
> In DFTB case, specifically, to find the file names to use DFTB first gets
> the atomic symbols from the atomic numbers. However, (obviously) the
> correspondence table does not have a symbol for atomic number “-1” or any
> other negative atomic number, and the function returns ‘^@^@‘ instead. Then
> DFTB tries to find the file with parameters for this and…
>
> DFTB does not check the atom names, because it allows the user to
> introduce parameters for new atoms just by downloading them from the
> DFTB.org, and the list of atoms can be updated regularly.
>
> A short term solution would be to edit the prmtop file directly to show
> the correct atomic numbers.
>
> Emilio: Does that seem to be the problem in your case as well? Does fixing
> the prmtop solves the problem?
>
> Gustavo Seabra
>
>
>
> > Em 05/10/2015, à(s) 16:02, Jonathan Sheehan <jonathan.sheehan.gmail.com>
> escreveu:
> >
> > Actually, these lines from the .prmtop file are probably more
> enlightening:
> >
> > %FLAG ATOMIC_NUMBER
> > %FORMAT(10I8)
> > -1 15 -1 -1 8 15 8 8 8
> 15
> > 8 8 8 6 1 1 6 1 8
> 6
> > 1 7 6 1 7 6 6 7 1
> 1
> > 7 6 1 7 6 6 1 8 1
> 6
> > 1 8 1
> >
> > I've attached the whole file for reference.
> >
> >
> >
> >
> > On Mon, Oct 5, 2015 at 1:28 PM, Jonathan Sheehan
> > <jonathan.sheehan.gmail.com> wrote:
> >> If it helps at all, I have observed something similar, using ATP.prep
> >> and frcmod.phos from here:
> >>
> >> http://www.pharmacy.manchester.ac.uk/bryce/amber/
> >>
> >> Details: I edited my input pdbfile so that the atomnames matched those
> >> in ATP.prep. (Interestingly, some atomnames include the * character,
> >> and others use the ' character.)
> >>
> >> My leap.in looks like this:
> >>
> >> source leaprc.ff14SB
> >> source leaprc.gaff
> >> loadamberparams frcmod.ionsjc_spce
> >> loadamberprep ../input_files/ATP.prep
> >> loadamberparams ../input_files/frcmod.phos
> >> x = loadpdb atp_lig.leap.input.pdb
> >> saveamberparm x atp_lig.noions.prmtop atp_lig.noions.crd
> >>
> >> The resulting .prmtop file contains these lines:
> >>
> >> %FLAG ATOM_NAME
> >> %FORMAT(20a4)
> >> O1G PG O2G O3G O3B PB O1B O2B O3A PA O1A O2A O5* C5* H50 H51 C4* H40
> O4* C1*
> >> H10 N9 C8 H80 N7 C5 C6 N6 H60 H61 N1 C2 H2 N3 C4 C3* H30 O3*
> H3' C2*
> >> H20 O2* H2'
> >>
> >> But the PDB file generated from that
> >> (ambpdb -p atp_lig.noions.prmtop -tit atp_lig.noions <
> >> atp_lig.noions.crd > atp_lig.noions.pdb)
> >> starts like this:
> >>
> >> ATOM 1 O1G atp 1 1.916 1.778 0.188 1.00 0.00
> ^.^.
> >> ATOM 2 PG atp 1 0.882 2.662 -0.036 1.00 0.00
> P
> >> ATOM 3 O2G atp 1 1.223 4.037 -0.058 1.00 0.00
> ^.^.
> >> ATOM 4 O3G atp 1 -0.263 2.056 0.601 1.00 0.00
> ^.^.
> >> ATOM 5 O3B atp 1 0.682 2.216 -1.708 1.00 0.00
> O
> >> ATOM 6 PB atp 1 0.675 2.954 -3.027 1.00 0.00
> P
> >> ATOM 7 O1B atp 1 0.233 4.294 -2.922 1.00 0.00
> O
> >> ATOM 8 O2B atp 1 0.025 1.895 -4.061 1.00 0.00
> O
> >> ATOM 9 O3A atp 1 2.396 2.980 -3.237 1.00 0.00
> O
> >>
> >> Admittedly, this is using a rather old (~May 2014) installation of
> >> AmberTools 14. Maybe this has already been fixed, but I thought it was
> >> odd that Emilio said his problem started with installing AmberTools
> >> 15.
> >>
> >> Hope that's helpful,
> >> -Jonathan
> >>
> >> --
> >> Jonathan Sheehan, Ph.D.
> >> Research Assistant Professor, Biochemistry
> >> Vanderbilt Univ. Ctr. for Structural Biology
> >> 5137 MRB3, 465 21st Avenue S.
> >> Nashville, TN 37240-7917
> >> Telephone: (615) 936-2516
> >> http://structbio.vanderbilt.edu/~sheehajh/
> >>
> >>
> >> On Mon, Oct 5, 2015 at 8:03 AM, Gustavo Seabra <
> gustavo.seabra.gmail.com> wrote:
> >>> Ok. Please keep us posted. If it turns out to be a bug, we can search
> for a
> >>> fix.
> >>>
> >>> Gustavo.
> >>> Em 05/10/2015 07:26, "Emilio Lence" <guitarro.de.meixente.gmail.com>
> >>> escreveu:
> >>>
> >>>> Hi Gustavo
> >>>> Thanks for your interest. A corrupted file was the fist suspicion
> that I
> >>>> have, but I'm not so sure that that is the issue here. It happen with
> >>>> different files, from different enzymes, different structures, and in
> all
> >>>> the cases the atoms that are misidentified are the 3 Oxygen atoms
> present
> >>>> in the gamma phosphate of the ATP. When I run AM1/d fails because
> assigned
> >>>> to the fist of this Oxygen atoms a Z number of -1. When I copied this
> files
> >>>> to another machine, the one that could be corrupted, it run without
> >>>> problems in several different machines, all with Amber12 installed.
> In my
> >>>> local machine with AmberTools15, other different types of enzyme run
> OK. Un
> >>>> fortunately, I have no access to a machine with the Ambertools14
> version. I
> >>>> will download and install it, and see what happens.
> >>>> I believe that there is a problem with the way the Oxygen atoms of
> the ATP
> >>>> are defined, that is no longer recognized by the new versions.
> >>>>
> >>>>
> >>>>
> >>>> 2015-10-02 21:51 GMT+02:00 Gustavo Seabra <gustavo.seabra.gmail.com>:
> >>>>
> >>>>> Hi Emilio,
> >>>>>
> >>>>> That shouldn’t happen, and it looks more like a case of corrupted
> file
> >>>>> somehow. Can you send me input input files so I can try them?
> >>>>>
> >>>>> Gustavo Seabra
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Em 02/10/2015, à(s) 15:11, Emilio Lence <
> >>>> guitarro.de.meixente.gmail.com>
> >>>>> escreveu:
> >>>>>>
> >>>>>> Dear amber users
> >>>>>> Recently I installed the AmberTools 15. When I tried to run a DFTB
> >>>>>> calculation with sander module, I couldn't. The reason is that do
> not
> >>>>>> recognised some atoms. In my case were 3 O atoms are recognised not
> as
> >>>>>> oxygen but as ^.^.. As a consequence I have an additional atom type
> (7
> >>>>>> instead of 6) with no parameters for it. I tried to copy de O-X.skf
> >>>> files
> >>>>>> as ^.^.-X.skf, but the sander module do not recognised the new files
> >>>>>> (although it ask for then). In previous versions of amber, you can
> run
> >>>>> the
> >>>>>> job without problem.
> >>>>>> I'm almost sure that I installed all the updates fro ambertools, but
> >>>>> right
> >>>>>> now I can't access the website of amber to check if there is son
> update
> >>>>>> related with this problem.
> >>>>>> Thanks for your kind attention
> >>>>>> Have a nice weekend
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Dr. Emilio Lence Quintana
> >>>>>> Organic Chemistry Department-CIQUS
> >>>>>> University of Santiago de Compostela
> >>>>>> 15782 Santiago de Compostela, Spain
> > <atp_lig.noions.prmtop>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Tue Oct 06 2015 - 05:00:03 PDT
