Re: [gmx-users] Topology include file "tip3p.itp" not found
On 11/8/18 5:20 AM, Rahma Dahmani wrote: Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with grompp) i get this error """ *atomtype OW is not found* then i create manually tip3p.itp file (which contains tip3p parameters) to identify the water atom types and i added in my topology file the following commands: ; Include water topology #include "tip3p.itp" But i always get this error Topology include file "tip3p.itp" not found If you #include a file without a path, grompp looks in the working directory or any directory specified by "include" in the .mdp file. -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.
[gmx-users] Topology include file "tip3p.itp" not found
Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with grompp) i get this error """ *atomtype OW is not found* then i create manually tip3p.itp file (which contains tip3p parameters) to identify the water atom types and i added in my topology file the following commands: ; Include water topology #include "tip3p.itp" But i always get this error Topology include file "tip3p.itp" not found Can you help me please, Thank you ! -- *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des Matériaux à l'état condensé, Laboratoire de Chimie Théorique et Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068, Tunisie Tél: (+216) 28151042* -- 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.
