On 1/17/18 9:35 AM, MD wrote:
Hi, so yesterday I left it moving forward to do the md.mdp. Very strangely,
the ring goes back to flat form after md.mdp. I am not quite sure what
happened here?
As I said yesterday, the topology you generated was based on incorrect
structure and inappropriate mixing of atom types. Whatever behavior it
exhibits is basically due to random chance unless you do the work to
parametrize it properly. Even if you get some serendipitous outcome,
don't trust it.
-Justin
Ming
On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
You still have many sources of problems (e.g. the warnings you suppressed,
the fact that your ring's atoms interact with an environment). What happens
when you minimize a capped peptide in vacuo?
Mark
On Tue, Jan 16, 2018 at 12:39 PM MD <refm...@gmail.com> wrote:
Hi Justin,
I got the itp and parameters of my side chain modified amino acid from
CHARMM-GUI and incorporated it into my protein structure, labeled with
HETATM. I made the atom types names consistent with charmm forcefield
which
I used with gromacs and made sure overall the parameters look decent for
now. After some fixing the grompp would run with no warnings, and I did a
quick energy minimization, but ended up with a distorted six member
ring. I
have the picture and my parameters attached. Your time is appreciated :)
https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-
rgIesxy0QdIHm7tqTug/edit?usp=sharing
Ming
On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/15/18 7:45 PM, MD wrote:
Hi Gromacs,
I have a modified side chain amino acid and it has a six member ring
attached to it. Regarding this ring I had dihedral angles taken care
with
some 0s and some 180s. However, after minimization my structure looks
very
strange, the ring is not flat and the dihedral angles in my settings
didn't
seem to apply to the minimized structure at all. Any thoughts?
You're going to have to provide a lot more detail. You're parametrizing
something nonstandard, so there are plenty of places to make mistakes.
Without knowing your structure, the actual parameters and how derived
and
validated them, there's nothing to do but guess.
Keep in mind that rings are not necessarily perfectly planar, and the
values set for dihedral phase offsets do not strictly mean the values
that
the dihedrals must adopt.
-Justin
--
==================================================
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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