On 7/5/15 12:56 AM, Christopher Neale wrote:
Dear Justin:
Thank you for your help. I am glad to see that I was not way out to lunch in my
interpretation of multiplicity and proper dihedral angles.
First, the out-of-plane motions are not minor. Even just in EM, the dihedral
angles along the main ring convert from near 0 deg to about 50 deg, so I think
that we're into the neighbourhood of major problems here. Second, my test
system was a single ring, like benzene but with a couple of substituents.
However, I can reproduce this issue in a standard molecule as follows, so I do
not think that the issue has anything to do with my exotic molecule. Take any
peptide/protein with a phenylalanine. There are 24 proper dihedral angles
around the PHE sidechain ring in the amber99 force field. In this force field,
these dihedral angles are all 180 deg / Fc=15.1669998 / mult=2. I take my
toplogy out of pdb2gmx and specify these parameters in the .top file and run EM
and I still get the planar ring, as expected. Now I simply change those N=24
occurrences of 180 deg to 0 deg (still multiplicity=2) and I run EM and I get
these ~50 deg dihedral angles around the ring. This is still wit!
h g
romacs 4.6.3. I have not checked with other versions of gromacs.
If you make a PHE-PHE peptide in VMD with molefacture (2 aa's to avoid the
problem amber has with a single amino acid and the termini), then run it
through pdb2gmx (v. 4.6.3) the lines in the [ dihedrals ] section that need
modification to adjust the proper dihedral angles in the ring of the first PHE
sidechain are:
7 10 11 12 9 0 15.1669998 2
7 10 11 13 9 0 15.1669998 2
19 10 11 12 9 0 15.1669998 2
19 10 11 13 9 0 15.1669998 2
7 10 19 17 9 0 15.1669998 2
7 10 19 20 9 0 15.1669998 2
11 10 19 17 9 0 15.1669998 2
11 10 19 20 9 0 15.1669998 2
10 11 13 14 9 0 15.1669998 2
10 11 13 15 9 0 15.1669998 2
12 11 13 14 9 0 15.1669998 2
12 11 13 15 9 0 15.1669998 2
11 13 15 16 9 0 15.1669998 2
11 13 15 17 9 0 15.1669998 2
14 13 15 16 9 0 15.1669998 2
14 13 15 17 9 0 15.1669998 2
13 15 17 18 9 0 15.1669998 2
13 15 17 19 9 0 15.1669998 2
16 15 17 18 9 0 15.1669998 2
16 15 17 19 9 0 15.1669998 2
15 17 19 10 9 0 15.1669998 2
15 17 19 20 9 0 15.1669998 2
18 17 19 10 9 0 15.1669998 2
18 17 19 20 9 0 15.1669998 2
Can you send the full topology, or at least the [atoms] section? I can't
decipher what these actually should be.
-Justin
where I get the bizarre conformations when I use the above, but if I switch the "0"'s to
"180"'s (recovering the original force field) then I get a planar ring.
Therefore, I think that either I am misunderstanding something about proper
dihedrals and multiplicity = 2 or there is a more serious problem. What I don't
understand at this point is that the force fields (amber at least) actually
contain quite a few proper dihedrals that do use angle = 0 and multiplicity =
2, so what is special aboutthe PHE test case outlined above that leads them to
not work whereas they are obviously intended to work.
I'll take a look into other gromacs versions when I have a chance and will
report back.
Thank you,
Chris.
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul
<jalem...@vt.edu>
Sent: 04 July 2015 09:41
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180
deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/4/15 3:32 AM, Christopher Neale wrote:
Dear Gromacs users:
I have been working on creating a topology for an exotic molecule. It
contains aromatic rings and my parameters always seemed to allow the rings to
buckle and become non-planer, much like a glucose ring would (though a little
less extensively). However, I have managed to solve the problem by switching
my proper (type 9) dihedral angles from angle = 0 degrees, multiplicity = 2
to angle = 180 degrees, multiplicity = 2. I thought that those two conditions
should be equivalent and it was only by seriously simplifying the molecule
down to a single ring and then toying with every conceivable parameter that I
even hit on this. I am using gromacs 4.6.3 and have not tried other versions
of gromacs, but this makes so little sense to me that I thought I would ask
about it here. There are lots of proper dihedrals in the available force
fields that use dihedrals with a set angle of zero degrees, though I do note
that for any aromatic ring that I have seen they are always 180 deg (with
mul tiplicity of 2 so that they can handle both cis and trans). Presumably I
have just missed some obvious definition, but at least I can verify that if I
switch even one proper dihedral from angle = 180 back to angle = 0 (with
multiplicity = 2 in each case), then I start to see deformation of the ring's
planarity.
Some deformation is not necessarily unphysical. Aromatic rings in CHARMM are
treated like this, for instance. It shouldn't be substantial, but it shouldn't
remain exactly planar, either. What are the parameters you're using? The
choice of 0 vs. 180 here for multiplicity = 2 should indeed be irrelevant. Have
you gone down to something as simple as, e.g. benzene?
-Justin
--
==================================================
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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