Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15

From: Jonathan Sheehan <jonathan.sheehan.gmail.com>
Date: Mon, 5 Oct 2015 13:28:04 -0500

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 - 11:30:04 PDT
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