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 <[email protected]> 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 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
