On 4/29/20 8:50 AM, Dutta, Kunal wrote:
Dear Friends, I'm trying to learn Tutorial 2: KALP15 in DPPC <http://www.mdtutorials.com/gmx/membrane_protein/index.html> The FOLLOWING PROBLEM APPEARS: " GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/kunal/Documents/MD_Simulation/B2AR in POPC Command line: gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -2044757183 Generated 837 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) *Fatal error:number of coordinates in coordinate file (popc128a.pdb, 14036) does not match topology (topol_popc.top, 17621)* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "
Likely you have specified the wrong number of water molecules in the topology. Don't adhere too closely to the tutorial when using different coordinate files (and lipids). There are probably a different number of waters in the POPC system so you will have to make more adjustments to the topology than might be immediately apparent.
-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.
