On 10/15/15 4:18 AM, Dries Van Rompaey wrote:
I did some more testing, it seems that this only occurs when the PRO
residue is preceded by a glycine. Could this be related to this issue:
http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I
change the glycine residue to anything else, pdb2gmx works like a charm. I
constructed a simple test system in which I can replicate the error (see
below).
Indeed, it seems that the AMBER03 version of GLY has a bunch of dihedrals
defined that shouldn't be. It also looks like it is the only AMBER force field
that does this, so it's clearly a mistake. I will submit a patch for the 5.1
series. Thanks for digging into this.
-Justin
REMARK 99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39
2015
ATOM 1 N ALA 1 0.268 -1.146 -1.547 1.00 0.00
N1+
ATOM 2 CA ALA 1 0.506 0.327 -1.714 1.00 0.00
C
ATOM 3 CB ALA 1 -0.837 1.004 -1.931 1.00 0.00
C
ATOM 4 C ALA 1 1.226 0.877 -0.480 1.00 0.00
C
ATOM 5 O ALA 1 1.399 0.165 0.509 1.00 0.00
O
ATOM 6 H1 ALA 1 -0.272 -1.324 -0.688 1.00 0.00
H
ATOM 7 H2 ALA 1 -0.224 -1.571 -2.343 1.00 0.00
H
ATOM 8 H3 ALA 1 1.161 -1.641 -1.413 1.00 0.00
H
ATOM 9 HA ALA 1 1.151 0.435 -2.592 1.00 0.00
H
ATOM 10 HB1 ALA 1 -1.364 0.570 -2.788 1.00 0.00
H
ATOM 11 HB2 ALA 1 -1.480 0.906 -1.049 1.00 0.00
H
ATOM 12 HB3 ALA 1 -0.710 2.074 -2.125 1.00 0.00
H
ATOM 13 N GLY 2 1.667 2.171 -0.583 1.00 0.00
N
ATOM 14 CA GLY 2 2.390 2.835 0.493 1.00 0.00
C
ATOM 15 C GLY 2 2.792 4.221 0.005 1.00 0.00
C
ATOM 16 O GLY 2 2.258 4.706 -0.997 1.00 0.00
O
ATOM 17 H GLY 2 1.519 2.744 -1.415 1.00 0.00
H
ATOM 18 HA1 GLY 2 1.730 2.918 1.361 1.00 0.00
H
ATOM 19 HA2 GLY 2 3.269 2.234 0.743 1.00 0.00
H
ATOM 20 N PRO 3 3.764 4.872 0.730 1.00 0.00
N
ATOM 21 CD PRO 3 4.331 4.472 2.006 1.00 0.00
C
ATOM 22 CG PRO 3 4.793 5.786 2.610 1.00 0.00
C
ATOM 23 CB PRO 3 5.270 6.581 1.399 1.00 0.00
C
ATOM 24 CA PRO 3 4.347 6.129 0.260 1.00 0.00
C
ATOM 25 C PRO 3 5.168 5.908 -1.021 1.00 0.00
C
ATOM 26 O PRO 3 5.520 4.796 -1.412 1.00 0.00
O
ATOM 27 HA PRO 3 3.538 6.843 0.069 1.00 0.00
H
ATOM 28 HB1 PRO 3 6.318 6.337 1.188 1.00 0.00
H
ATOM 29 HB2 PRO 3 5.212 7.661 1.568 1.00 0.00
H
ATOM 30 HG1 PRO 3 5.571 5.654 3.367 1.00 0.00
H
ATOM 31 HG2 PRO 3 3.945 6.303 3.076 1.00 0.00
H
ATOM 32 HD1 PRO 3 5.175 3.804 1.803 1.00 0.00
H
ATOM 33 HD2 PRO 3 3.599 3.952 2.629 1.00 0.00
H
ATOM 34 N ALA 4 5.499 7.083 -1.656 1.00 0.00
N
ATOM 35 CA ALA 4 6.262 7.165 -2.905 1.00 0.00
C
ATOM 36 CB ALA 4 5.416 6.725 -4.094 1.00 0.00
C
ATOM 37 C ALA 4 6.738 8.618 -3.177 1.00 0.00
C
ATOM 38 OXT ALA 4 7.513 8.768 -4.161 1.00 0.00
O1-
ATOM 39 O ALA 4 6.290 9.477 -2.354 1.00 0.00
O
ATOM 40 H ALA 4 5.250 8.002 -1.288 1.00 0.00
H
ATOM 41 HA ALA 4 7.137 6.512 -2.806 1.00 0.00
H
ATOM 42 HB1 ALA 4 4.539 7.372 -4.215 1.00 0.00
H
ATOM 43 HB2 ALA 4 5.988 6.759 -5.027 1.00 0.00
H
ATOM 44 HB3 ALA 4 5.053 5.700 -3.965 1.00 0.00
H
TER 45 ALA 4
END
On 8 October 2015 at 14:15, Dries Van Rompaey <dries.vanromp...@gmail.com>
wrote:
I definitely agree that it's odd that the warning only occurs with this
specific residue. I ran a diff against the freshly downloaded AMBER03
files, but they were identical. I also tried running it again with freshly
downloaded amber03 files in the directory.
About the error: pdb2gmx never crashed. It always runs to completion and
mentions that the topology was successfully generated. I only get a warning
during the execution of pdb2gmx.
Thanks for all your help,
Dries
On 8 October 2015 at 13:33, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/8/15 1:54 AM, Dries Van Rompaey wrote:
Thanks for the reply Justin. I unfortunately cannot currently disclose
the
files that I'm working on. Based on the info presented, would you say
that
it's an issue with the force field definition or with the actual protein
topology? I am not planning on using amber03 in my simulations at the
moment, so this specific warning is not that important, but I can't help
but wonder if this warning means something is off in the topology.
Given that error, there is no topology produced, so there's not going to
be a problem with the topology itself.
I'm sorry to say that without your actual files, there's literally
nothing we can do to diagnose this. You say some prolines work with
AMBER03 and others don't, which makes no sense at all. Either the .rtp is
sound or it isn't. Either it is unmodified (which will work) or someone has
tampered with it and broken it.
If you're not going to use AMBER03 and the topology is produced with
other force fields, then you know you have a problem with a hacked AMBER03
.rtp file. It should be very straightforward to simply to a diff against
the unmodified version (which you can get by downloading a fresh GROMACS
tarball if you don't already have it).
-Justin
On 7 October 2015 at 23:05, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/7/15 5:03 PM, Dries Van Rompaey wrote:
Thanks Justin, that makes sense! I'm wondering why none of the other
proline residues triggered that warning though? The same procedure
works
like a charm with other proteins.
Without access to all of the files you're looking at, the best I can do
is
shrug my shoulders because that doesn't make any sense. Some prolines
work
and one doesn't? That's just not logical.
-Justin
On 7 Oct 2015 10:59 pm, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 10/7/15 3:01 PM, Dries Van Rompaey wrote:
Hi Mark,
This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.
Non-terminal proline does not have an amide H. If your force field
.rtp
file claims to use such an atom used in a dihedral (which is what the
error
message tells you is happening), find out who altered the file and
reprimand them :)
-Justin
Kind regards,
Dries
On 7 October 2015 at 20:56, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Is it terminal? Are there specbonds in play? What's the GROMACS
version?
What's your pdb2gmx command line? :-)
Mark
On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
dries.vanromp...@gmail.com>
wrote:
Hi everyone,
I'm getting the following warning when I try to run pdb2gmx on my
protein
structure:
WARNING: WARNING: Residue 168 named PRO of a molecule in the input
file
was
mapped to an entry in the topology database, but the atom H used in
an
interaction of type dihedral in that entry is not found in the
input
file.
Perhaps your atom and/or residue naming needs to be fixed.
This warning is only present when I use the AMBER03 forcefield, all
other
forcefields seem to work fine. I have tried this with both a
structure
without hydrogens as well as a structure with hydrogens added, both
with
and without the -ignh flag. I tried looking at the amber03 database
files
as well as the amber99sb-ildn database files (amber99sb-ildn works
just
fine), but I could not find any reason why this particular residue
would
be
problematic. pdb2gmx does not find any problems with the other
proline
residues in the protein (which look identical), so I am puzzled as
to
what's causing this.
The proline residue is:
ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63
N
ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63
C
ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63
C
ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63
C
ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63
C
ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63
C
ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63
O
Does anyone know what's going on here?
Thanks in advance!
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Department of Pharmaceutical Sciences
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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