[gmx-users] Ryckaert-Bellemans Dihedral with AMBER

[tarak karmakar]

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.

Any suggestions?

Thanks & regards,
Tarak




On Wed, Mar 26, 2014 at 11:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/26/14, 1:30 PM, tarak karmakar wrote:
>
>> Dear All,
>> I need to use one Ryckaert-Bellemans dihedral type of a dihedral in a new
>> molecule. To do so, I'm including all the coefficients in .rtp file as
>> given below, (after bonds section)
>>
>> [dihedrals]
>>          HX   CX    CX   OX    3  -7.70990 -10.7269 -15.2261 -2.2442
>> -0.25839 0.0000
>>
>> The Force field I'm using for the protein is the amber99sb-ildn.ff.
>> I have  read an old post [
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
>> users/2013-April/080306.html]
>> in the mailing list and got some clues about how to use this kind of
>> dihedral forms. Accordingly I have approached.
>>
>> But at the end I've got the following error,
>> "No default Proper Dih. types"
>>
>> Do I need to do something more?
>> Could anyone guide me the proper way of implementing it?
>>
>>
> Are the parameters for that dihedral written to the .top?  A [dihedrals]
> entry in an .rtp file maps to the .top, but normally parameters are not
> explicitly defined in the .rtp.  The parameters are defined in ffbonded.itp
> and grompp looks them up.  If they are present in the .top, there's no
> reason for grompp to (1) go looking for them or (2) think the dihedral is
> periodic.  Probably the conflict comes from the fact that the parent force
> field is structured for type 9 periodic dihedrals, but in principle you
> should be able to add whatever you want.
>
> -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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