Gustavo,
Thanks for the work-around. Yes, editing the .prmtop file works for
me, too. (It produces .pdb files that don't confuse PyMOL.) But just
to be clear, is this a (minor) bug, or am I doing something wrong?
The .prep and .frcmod files both refer to the atomtype "O3". They
don't specify its atomic number, and I don't see a way to add that,
using the current .frcmod format.
For anyone else running into this problem: you can use cpptraj in
place of ambpdb. It seems to take the .prmtop with (-1) in the
ATOMIC_NUMBER positions for O3, and produce a .pdb file that correctly
has O in the element column. Magic! (Maybe it keys off the mass?)
and Emilio,
Thank you for sharing your experience with ATP. Could you let us know
if you find any other ATP parameters which do not give O-P distances
that are too short? (Just using MM, not QM.)
Thanks,
-J'n
On Tue, Oct 6, 2015 at 6:54 AM, Emilio Lence
<guitarro.de.meixente.gmail.com> wrote:
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 07 2015 - 14:00:04 PDT
