[gmx-users] Ryckaert-Bellemans Dihedral with AMBER

[Justin Lemkul]

On 3/27/14, 12:19 AM, tarak karmakar wrote:
> Thanks Justin for looking at the problem.
> No, the dihedral information is not written in the .top file.
> I've tried to include the RB dihedral info into the 'ffbonded.itp' file but
> even then it did not consider it.
> Yes, the parent force field has the type '9'.
>
> I added a line containing the dihedral at the bottom of the ffbonded.itp
> (amber99sb-ildn.ff) file and then tried to proceed.
>
> #define torsion_ASN_CA_CB_CG_ND2_mult1         0.0        -4.376464
> 1  ; Proteins 78, 1950 (2010)
> #define torsion_ASN_CA_CB_CG_ND2_mult2         0.0        -0.757304
> 2  ; Proteins 78, 1950 (2010)
> #define torsion_ASN_CA_CB_CG_ND2_mult3         0.0        -0.146440
> 3  ; Proteins 78, 1950 (2010)
> #define torsion_ASN_CA_CB_CG_ND2_mult4         0.0         0.418400
> 4  ; Proteins 78, 1950 (2010)
> #define torsion_ASN_CA_CB_CG_ND2_mult5         0.0         0.543920
> 5  ; Proteins 78, 1950 (2010)
> #define torsion_ASN_CA_CB_CG_ND2_mult6         0.0        -0.443504
> 6  ; Proteins 78, 1950 (2010)
>
> ;amber tarak added
> HX   CX    CX   OX    3  -7.70990 -10.7269 -15.2261 -2.2442 -0.25839 0.0000
>
> This also failed.
>

Please define "failed" - the same error message?

> Any suggestions?
>

It *should* be possible to add whatever interactions you like, but maybe there's 
some quirk here that I'm unaware of.  OPLS-AA, for instance, has both periodic 
(type 1) and R-B (type 3) dihedrals, so in principle it can be done.  Maybe 
there's something special about force fields that use type 9 periodic dihedrals 
(because those are special, anyway), so that could very well be it.  I haven't 
gone into that part of the code (and don't intend to any time soon), so perhaps 
someone else has some insight here.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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