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
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Received on Mon Oct 05 2015 - 12:30:03 PDT
