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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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
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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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