On 4/29/20 8:50 AM, Dutta, Kunal wrote:
Dear Friends,
I'm trying to learn Tutorial 2: KALP15 in DPPC

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 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


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