On 4/26/20 5:15 AM, Paolo Costa wrote:
Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got the following fatal error: "*Atom O10 in residue POM 0 was not found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea what the warning means, however I do not understand the fatal error since I am sure that the Atom O1 is present in the residue I created. In attachment you can find the .pdb and the .rtp files I created.
The mailing list does not accept attachments. If you want to share files, upload them to a file-sharing service and provide a link. Note that the error mentions O10, not O1.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.