On 1/22/18 2:20 AM, Sailesh Bataju wrote:
Hi, I have been trying to simulate isobutane in urea as a solvent. I have made myself urea.itp and urea.gro file for charmm36 forcefield under equilibrating at certain temperature and pressure. First nvt followed by npt I got error like this while equilibriating. Program: gmx grompp, version 2018 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008) Fatal error: Cannot find position restraint file restraint.gro (option -r). From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Despite of this error, I continue comment define= -DPOSRE in .mdp file. Then the simulation run smoothly without any error. After urea has been equilibriated in a box under certain temperature and pressure . Now i've to put isobutane molecule in it. There has been no error till energy minimization. But when i've to equilibriate in nvt, I got error like this. GROMACS: gmx grompp, version 2018 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/sailesh/Documents/Thesis/urea_1000 Command line: gmx grompp -f nvt_urea.mdp -c em_urea.gro -p topol.top -o nvt_urea.tpr Ignoring obsolete mdp entry 'title' Generated 85052 of the 85078 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 55198 of the 85078 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Alkane_chain_A' Excluding 3 bonded neighbours molecule type 'Urea' Velocities were taken from a Maxwell distribution at 298 K Removing all charge groups because cutoff-scheme=Verlet ------------------------------------------------------- Program: gmx grompp, version 2018 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008) Fatal error: Cannot find position restraint file restraint.gro (option -r). From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- turning all bonds into constraints... turning all bonds into constraints... This is my end part of topol.top file for isobutane in urea. ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include urea topology #include "charmm36.ff/urea.itp" #ifdef POSRES #include "posre_urea.itp" #endif ; Include topology for ions #include "charmm36.ff/ions.itp" [ system ] ; Name Isobutane in Urea [ molecules ] ; Compound #mols Alkane_chain_A 2 Urea 841 Any idea to solve this problem.
The error message tells you exactly what to do (it's probably one of the most verbose error messages I've ever seen). The -r argument is now required.
-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.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.