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

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

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