On 11/5/18 12:16 PM, Karpurmanjari Kakati wrote:
Dear Justin, I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the aminoacids.rtp file . I have all the files of OPLS AA force field in my working directory. For that I tried to generate the initial rtp format file from the hydroxy proline's .pdb and .gro files using the following command: gmx x2top -f hyd.gro -r hyd.rtp -pbc -ff oplsaa and I got the following error: Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 name to type translations in file oplsaa.ff Generating bonds from distances... atom 18 Can not find forcefield for atom CA-2 with 4 bonds Can not find forcefield for atom C-3 with 3 bonds Can not find forcefield for atom CD-7 with 4 bonds ------------------------------------------------------- Program: gmx x2top, version 2018.1 Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 205) Fatal error: Could only find a forcefield type for 15 out of 18 atoms. Can you help me with this. I want to add this residue to the rtp file so that I can use the step pdb2gmx directly.
You don't need x2top. Just make a copy of the PRO residue to something like HYP and modify it accordingly. You're doing a lot of extra work trying to get a functional .n2t file for a straightforward modification of an existing residue. You must already know the atom types and charges if you're trying to put them in an .n2t file, so cut out the middleman and just do it directly.
-Justin -- ================================================== 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.
