[gmx-users] Missing bond

[Sudip Das]

Dear Justin,

Thanks for your kind help!

Best regards,
Sudip




On Mon, Apr 3, 2017 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/1/17 1:18 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> While I am preparing my system topology with pdb2gmx for a system
>> containing enzyme with 30 non-ionic surfactant molecules in water, I got
>> 36
>> number of bonds per surfactant molecules, but actually it has 37 bonds
>> (anyways, the number of angle, dihedral etc. are correct). From the
>> generated topology for this surfactant, I found out the missing bond. But
>> I
>> checked that I have incorporated that bond in aminoacids.rtp file and that
>> bond type is also present in the ffbonded.itp file.
>>
>> To figure out the reason, I used the pdb2gmx for a system with only 30
>> surfactant molecules in water (no enzyme). Again I encountered the same
>> problem.
>>
>> So, what could be the solution? Please assist me.
>>
>>
> Something does not add up.  Angles and dihedrals are built from the bonds,
> so if there's a bond missing, the angles and dihedrals shouldn't be right.
> Which bond is missing?  If it's in the .rtp there's no way it is somehow
> ignored while the others get processed correctly.
>
> -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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