On 3/29/15 4:07 PM, Alex wrote:
Hi all, I am messing with the OPLS/AA forcefield. The idea is to functionalize graphene edge atoms beyond passivation with hydrogen. At the functionalization region, there is a C atom with two C-C bonds (from graphene), while the third bond is formed with the functional group. The particular atom from the functional group intended to bond with that C bond is also carbon. When setting up the system, in atomname2type.n2t I have: CJ opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 ; bulk graphene C but also want to introduce CJ opls_1001 0.1 12.011 3 C 0.142 C 0.142 C 0.149 ; edge C Both 996 and 1001 are defined in the ffnononbonded.itp, these are custom, but essentially copies from oplsaa entries for carbon. Note the third bond that's longer (which is also the case in my input PDB). The significant difference is of course the charge there, as I want a globally neutral system. Here is the problem: x2top ignores the second statement from above and the functionalized edge C is assigned #996. Aside from manually modifying the resulting topology, can we make this distinction stick?
g_x2top (and other programs like pdb2gmx) use a default ± 10% distance tolerance for deciding if something is within bonding distance. The distinction between 0.149 and 0.142 is about 5%, so the two lines are effectively indistinguishable. The most straightforward solution would be to change the default tolerance in the code, if your distances are going to be so close in magnitude.
-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 [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].
