[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?
Christopher Neale
chris.neale at alum.utoronto.ca
Sun Jul 5 15:10:20 CEST 2015
Dear Justin:
here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace "0 15.1669998 2" by "180 15.1669998 2" and everything is groovy.
Chris.
###########################################
### TOPOLOGY
;
; File 'topol.top' was generated
; By user: lh824914 (36108)
; On host: headnode.rit.albany.edu
; At date: Sat Jul 4 23:10:10 2015
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.6.3
;
; Command line was:
; pdb2gmx -f FF.gro -ignh
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 PHE rtp NPHE q +1.0
1 N3 1 PHE N 1 0.1737 14.01 ; qtot 0.1737
2 H 1 PHE H1 2 0.1921 1.008 ; qtot 0.3658
3 H 1 PHE H2 3 0.1921 1.008 ; qtot 0.5579
4 H 1 PHE H3 4 0.1921 1.008 ; qtot 0.75
5 CT 1 PHE CA 5 0.0733 12.01 ; qtot 0.8233
6 HP 1 PHE HA 6 0.1041 1.008 ; qtot 0.9274
7 CT 1 PHE CB 7 0.033 12.01 ; qtot 0.9604
8 HC 1 PHE HB1 8 0.0104 1.008 ; qtot 0.9708
9 HC 1 PHE HB2 9 0.0104 1.008 ; qtot 0.9812
10 CA 1 PHE CG 10 0.0031 12.01 ; qtot 0.9843
11 CA 1 PHE CD1 11 -0.1392 12.01 ; qtot 0.8451
12 HA 1 PHE HD1 12 0.1374 1.008 ; qtot 0.9825
13 CA 1 PHE CE1 13 -0.1602 12.01 ; qtot 0.8223
14 HA 1 PHE HE1 14 0.1433 1.008 ; qtot 0.9656
15 CA 1 PHE CZ 15 -0.1208 12.01 ; qtot 0.8448
16 HA 1 PHE HZ 16 0.1329 1.008 ; qtot 0.9777
17 CA 1 PHE CE2 17 -0.1603 12.01 ; qtot 0.8174
18 HA 1 PHE HE2 18 0.1433 1.008 ; qtot 0.9607
19 CA 1 PHE CD2 19 -0.1391 12.01 ; qtot 0.8216
20 HA 1 PHE HD2 20 0.1374 1.008 ; qtot 0.959
21 C 1 PHE C 21 0.6123 12.01 ; qtot 1.571
22 O 1 PHE O 22 -0.5713 16 ; qtot 1
; residue 2 PHE rtp CPHE q -1.0
23 N 2 PHE N 23 -0.3821 14.01 ; qtot 0.6179
24 H 2 PHE H 24 0.2681 1.008 ; qtot 0.886
25 CT 2 PHE CA 25 -0.1825 12.01 ; qtot 0.7035
26 H1 2 PHE HA 26 0.1098 1.008 ; qtot 0.8133
27 CT 2 PHE CB 27 -0.0959 12.01 ; qtot 0.7174
28 HC 2 PHE HB1 28 0.0443 1.008 ; qtot 0.7617
29 HC 2 PHE HB2 29 0.0443 1.008 ; qtot 0.806
30 CA 2 PHE CG 30 0.0552 12.01 ; qtot 0.8612
31 CA 2 PHE CD1 31 -0.13 12.01 ; qtot 0.7312
32 HA 2 PHE HD1 32 0.1408 1.008 ; qtot 0.872
33 CA 2 PHE CE1 33 -0.1847 12.01 ; qtot 0.6873
34 HA 2 PHE HE1 34 0.1461 1.008 ; qtot 0.8334
35 CA 2 PHE CZ 35 -0.0944 12.01 ; qtot 0.739
36 HA 2 PHE HZ 36 0.128 1.008 ; qtot 0.867
37 CA 2 PHE CE2 37 -0.1847 12.01 ; qtot 0.6823
38 HA 2 PHE HE2 38 0.1461 1.008 ; qtot 0.8284
39 CA 2 PHE CD2 39 -0.13 12.01 ; qtot 0.6984
40 HA 2 PHE HD2 40 0.1408 1.008 ; qtot 0.8392
41 C 2 PHE C 41 0.766 12.01 ; qtot 1.605
42 O2 2 PHE OC1 42 -0.8026 16 ; qtot 0.8026
43 O2 2 PHE OC2 43 -0.8026 16 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 21 1
7 8 1
7 9 1
7 10 1
10 11 1
10 19 1
11 12 1
11 13 1
13 14 1
13 15 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
21 22 1
21 23 1
23 24 1
23 25 1
25 26 1
25 27 1
25 41 1
27 28 1
27 29 1
27 30 1
30 31 1
30 39 1
31 32 1
31 33 1
33 34 1
33 35 1
35 36 1
35 37 1
37 38 1
37 39 1
39 40 1
41 42 1
41 43 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
1 10 1
1 22 1
1 23 1
2 6 1
2 7 1
2 21 1
3 6 1
3 7 1
3 21 1
4 6 1
4 7 1
4 21 1
5 11 1
5 19 1
5 24 1
5 25 1
6 8 1
6 9 1
6 10 1
6 22 1
6 23 1
7 12 1
7 13 1
7 17 1
7 20 1
7 22 1
7 23 1
8 11 1
8 19 1
8 21 1
9 11 1
9 19 1
9 21 1
10 14 1
10 15 1
10 18 1
10 21 1
11 16 1
11 17 1
11 20 1
12 14 1
12 15 1
12 19 1
13 18 1
13 19 1
14 16 1
14 17 1
15 20 1
16 18 1
16 19 1
18 20 1
21 26 1
21 27 1
21 41 1
22 24 1
22 25 1
23 28 1
23 29 1
23 30 1
23 42 1
23 43 1
24 26 1
24 27 1
24 41 1
25 31 1
25 39 1
26 28 1
26 29 1
26 30 1
26 42 1
26 43 1
27 32 1
27 33 1
27 37 1
27 40 1
27 42 1
27 43 1
28 31 1
28 39 1
28 41 1
29 31 1
29 39 1
29 41 1
30 34 1
30 35 1
30 38 1
30 41 1
31 36 1
31 37 1
31 40 1
32 34 1
32 35 1
32 39 1
33 38 1
33 39 1
34 36 1
34 37 1
35 40 1
36 38 1
36 39 1
38 40 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 21 1
6 5 7 1
6 5 21 1
7 5 21 1
5 7 8 1
5 7 9 1
5 7 10 1
8 7 9 1
8 7 10 1
9 7 10 1
7 10 11 1
7 10 19 1
11 10 19 1
10 11 12 1
10 11 13 1
12 11 13 1
11 13 14 1
11 13 15 1
14 13 15 1
13 15 16 1
13 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
10 19 17 1
10 19 20 1
17 19 20 1
5 21 22 1
5 21 23 1
22 21 23 1
21 23 24 1
21 23 25 1
24 23 25 1
23 25 26 1
23 25 27 1
23 25 41 1
26 25 27 1
26 25 41 1
27 25 41 1
25 27 28 1
25 27 29 1
25 27 30 1
28 27 29 1
28 27 30 1
29 27 30 1
27 30 31 1
27 30 39 1
31 30 39 1
30 31 32 1
30 31 33 1
32 31 33 1
31 33 34 1
31 33 35 1
34 33 35 1
33 35 36 1
33 35 37 1
36 35 37 1
35 37 38 1
35 37 39 1
38 37 39 1
30 39 37 1
30 39 40 1
37 39 40 1
25 41 42 1
25 41 43 1
42 41 43 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 9
2 1 5 7 9
2 1 5 21 9
3 1 5 6 9
3 1 5 7 9
3 1 5 21 9
4 1 5 6 9
4 1 5 7 9
4 1 5 21 9
1 5 7 8 9
1 5 7 9 9
1 5 7 10 9
6 5 7 8 9
6 5 7 9 9
6 5 7 10 9
21 5 7 8 9
21 5 7 9 9
21 5 7 10 9
1 5 21 22 9
1 5 21 23 9
6 5 21 22 9
6 5 21 23 9
7 5 21 22 9
7 5 21 23 9
5 7 10 11 9
5 7 10 19 9
8 7 10 11 9
8 7 10 19 9
9 7 10 11 9
9 7 10 19 9
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
5 21 23 24 9
5 21 23 25 9
22 21 23 24 9
22 21 23 25 9
21 23 25 26 9
21 23 25 27 9
21 23 25 41 9
24 23 25 26 9
24 23 25 27 9
24 23 25 41 9
23 25 27 28 9
23 25 27 29 9
23 25 27 30 9
26 25 27 28 9
26 25 27 29 9
26 25 27 30 9
41 25 27 28 9
41 25 27 29 9
41 25 27 30 9
23 25 41 42 9
23 25 41 43 9
26 25 41 42 9
26 25 41 43 9
27 25 41 42 9
27 25 41 43 9
25 27 30 31 9
25 27 30 39 9
28 27 30 31 9
28 27 30 39 9
29 27 30 31 9
29 27 30 39 9
27 30 31 32 9
27 30 31 33 9
39 30 31 32 9
39 30 31 33 9
27 30 39 37 9
27 30 39 40 9
31 30 39 37 9
31 30 39 40 9
30 31 33 34 9
30 31 33 35 9
32 31 33 34 9
32 31 33 35 9
31 33 35 36 9
31 33 35 37 9
34 33 35 36 9
34 33 35 37 9
33 35 37 38 9
33 35 37 39 9
36 35 37 38 9
36 35 37 39 9
35 37 39 30 9
35 37 39 40 9
38 37 39 30 9
38 37 39 40 9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 23 21 22 4
7 10 19 11 4
10 13 11 12 4
10 17 19 20 4
11 15 13 14 4
13 17 15 16 4
15 19 17 18 4
21 25 23 24 4
25 42 41 43 4
27 30 39 31 4
30 33 31 32 4
30 37 39 40 4
31 35 33 34 4
33 37 35 36 4
35 39 37 38 4
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber99.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber99.ff/ions.itp"
[ system ]
; Name
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
[ molecules ]
; Compound #mols
Protein 1
###########################################
### INITIAL COORDINATES
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
43
1PHE N 1 -0.013 0.245 -0.011
1PHE H1 2 -0.082 0.296 0.040
1PHE H2 3 0.064 0.225 0.049
1PHE H3 4 0.018 0.300 -0.088
1PHE CA 5 -0.070 0.121 -0.060
1PHE HA 6 -0.146 0.146 -0.120
1PHE CB 7 0.036 0.047 -0.136
1PHE HB1 8 0.122 0.085 -0.102
1PHE HB2 9 0.023 0.076 -0.231
1PHE CG 10 0.058 -0.104 -0.142
1PHE CD1 11 -0.017 -0.189 -0.060
1PHE HD1 12 -0.085 -0.151 0.003
1PHE CE1 13 0.003 -0.327 -0.067
1PHE HE1 14 -0.051 -0.388 -0.009
1PHE CZ 15 0.098 -0.380 -0.155
1PHE HZ 16 0.112 -0.479 -0.160
1PHE CE2 17 0.173 -0.294 -0.237
1PHE HE2 18 0.241 -0.331 -0.300
1PHE CD2 19 0.152 -0.155 -0.230
1PHE HD2 20 0.205 -0.093 -0.288
1PHE C 21 -0.122 0.034 0.054
1PHE O 22 -0.052 -0.053 0.105
2PHE N 23 -0.243 0.056 0.096
2PHE H 24 -0.298 0.127 0.053
2PHE CA 25 -0.300 -0.022 0.206
2PHE HA 26 -0.301 -0.118 0.177
2PHE CB 27 -0.214 -0.007 0.327
2PHE HB1 28 -0.258 0.067 0.379
2PHE HB2 29 -0.127 0.025 0.291
2PHE CG 30 -0.179 -0.115 0.430
2PHE CD1 31 -0.241 -0.240 0.424
2PHE HD1 32 -0.309 -0.259 0.353
2PHE CE1 33 -0.208 -0.338 0.518
2PHE HE1 34 -0.252 -0.428 0.514
2PHE CZ 35 -0.113 -0.311 0.618
2PHE HZ 36 -0.090 -0.381 0.685
2PHE CE2 37 -0.051 -0.185 0.623
2PHE HE2 38 0.016 -0.165 0.694
2PHE CD2 39 -0.084 -0.087 0.528
2PHE HD2 40 -0.040 0.003 0.531
2PHE C 41 -0.442 0.022 0.236
2PHE OC1 42 -0.493 -0.024 0.309
2PHE OC2 43 -0.496 0.113 0.173
10.00000 10.00000 10.00000
________________________________________
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: 05 July 2015 08:52
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 7/5/15 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
>
> ==================================================
> --
> Gromacs Users mailing list
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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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