[gmx-users] Plus / Minus sign in rtp file

[Mark Abraham]

Hi,

Your objective isn't clear. The + and - mechanism makes links between
polymer subunits - is that the role of your benzene?

Mark

On Mon, Jul 18, 2016 at 4:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/18/16 9:55 AM, Li, Shi wrote:
> > Dear Gmx users,
> >
> > I have a problem with the plus and minus signs while editing the .rtp
> file.
> > In the manual, it mentioned that it refers to the previous and next
> > residue. But what is the rule to include this? Say i have a benzene and
> on
> > C1 and C3 both bonded with a same residue. How should I include the
> > plus/minus? I had many trails and each time the residues will both bonded
> > with the same carbon (C1), leading to a long bond in the topology.
> > This is an example I used in the. rtp file. Can anyone tell my why this
> is
> > wrong and what is the rule?
> >
>
> Next residue = current residue index + 1
> Previous residue = current residue index - 1
>
> See existing amino acids for straightforward examples.
>
> > ;Benzene
> >
> > [ bonds ]
> > ....
> >   C1  +CT
> >  -CT  C3
>
> So this says: (res i-1)--CT-|-C3--(res i)--C1-|-CT--(res i+1)
>
> Your approach implies a branch point at CT, with both C1 and C3 of each
> residue
> bonding to the same atom (CT).  This may or may not be what you want.
>
> > ...
> > [ residue ]
> > ...
> >   CT  +C3
> >   CT   -C1
>
> I don't know what this is, as "residue" is not a valid directive.  Only
> bonded
> interactions (bonds, angles, dihedrals) can make use of the +/- mechanism.
>
> -Justin
>
> > ....
> > ....
> >
> > Many thanks,
> > Shi
> >
>
> --
> ==================================================
>
> 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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