[gmx-users] Ryckaert-Bellemans Dihedral with AMBER

[tarak karmakar]

"failed" with the same error.
"No default Proper Dih. types"

I was trying to make an .itp file as ligand.itp and then define the
dihedral in OPLS (3) RB style. Then I kept it in the oplsaa.ff directory
and gave the path into the .top file (include). But still I'm not able to
solve this.
I'll try little more and then possibly update this post.

Thanks Justin.

regards,
Tarak


On Thu, Mar 27, 2014 at 6:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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