I use x2top a whole lot, so here's an example to be considered in the context of what Justin just wrote:
CJ opls_xxx 0.0 12.011 3 CJ 0.142 CJ 0.142 CJ 0.142 The total number of bonds is 3, then just list them in pairs of element-bond entries. If I want a different type assigned to an atom that only has two nearest neighbors, it'd look like: CJ opls_yyy 0.0 12.011 2 CJ 0.142 CJ 0.142 and so on. A very useful utility for doing solid-state stuff with gmx. Hope this helps. Alex The On Mon, Sep 24, 2018 at 7:48 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/24/18 9:42 PM, paul buscemi wrote: > > This is a version of a very old question > > > > Using Avogadro, I’ve built an all atom version of nylon12, ( 45 atoms ) > converted to a gro file with editconf. I want to generate the rtp so I can > construct a polymer. Using x2top, I’ve tried using both gromos 54a7 ff > and oplsaaff. there are two outcomes: > > > > 1) if trying 54a7, I am warned that the atomnames2types.n2t is not > found ( and indeed it is not present in the ff subfolder ) . I’ve done > what I think is an extensive search ( eg github, etc ), but have not found > a n2t for 54a7. I tried to construct one following that found in oplsaa > but that has not worked out -yet. Does 54a7ff require an n2t file and if > so what is the format ? > > x2top requires an .n2t file for any force field. > > Sadly, my wiki page on .n2t files was somehow lost, so I will try to > repeat it here, in column numbers: > > 1. Element (e.g. first character of the atom name) > 2. Atom type to be assigned > 3. Charge to be assigned > 4. Mass > 5. Number of bonds the atom forms > 6-onward. The element and reference bond length for N bonds (where N is > specified in column 5); x2top will assign a bond if the detected > interatomic distance is within 10% of the reference bond length > specified here. > > > 2) In trying oplsaa, I am warned only 44 of 45 atom types are found.. > It turns out that it is the Nitrogen that is the culprit. If I convert the > nitrogen to carbon in the gro , file the top and rtp are completed. It’s > hard to believe that an amide nitrogen is not in the force field. Thinking > it may be my model, I downloaded arginine from “aminoacidsguide.com” to > avoid Avogadro. With Aginine only 19 of 26 atoms were found in the > oplassff. What ? I can’t make an rtp for arginine without modifying the > ffbonded or n2t for oplsaa. Is x2top simply not the right tool ? > > It's not that the atom type isn't found, it's that x2top can't assign an > atom type because a given atom does not satisfy all of the requirements > of the .n2t file listed above. That means a bond tolerance likely isn't > being satisfied. > > -Justin > > > Note if I submit the nylon pdb to ATB get back a usable itp, and it is > possible to generate a small polymer this way, ( 20 mers or so ). But I > should be able to construct a polymer similar to the example given for PE > some 9 years ago using a beginning, middle mers. But I need the rtp. > > > > Thanks for any responses > > Paul Buscemi, Ph.D. > > UMN > > > > > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.