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

[Justin Lemkul]

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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