On 9/20/18 5:01 PM, BIJENDRA KHADKA wrote:
Dear Justin, Thank you for your suggestion. I tried to process the ligand(NAD) with pdb2gmx, however, received the following error despite correct atom name in PDB file (file attached) relative to NAD information in merged.itp. In case of CHARMM-GUI, it provides a NAD.rtf and .prm as output, while Gromacs required an .itp as input. (How to convert .rtf file to .itp file).
You can't; a CHARMM .rtf is the equivalent of a GROMACS .rtp, not .itp. Besides, CHARMM-GUI provides you with all the files you need to run in GROMACS. Don't try to re-execute pdb2gmx. Just use the files it gives you.
-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.
