[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?

Justin Lemkul jalemkul at vt.edu
Sun Jul 5 14:52:42 CEST 2015 


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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: 04 July 2015 09:41
> To: gmx-users at 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
>
> jalemkul at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

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