Re: [gmx-users] POPC: Fatal error:

[Justin Lemkul]

On 4/29/20 8:50 AM, Dutta, Kunal wrote:

Dear Friends,
I'm trying to learn Tutorial 2: KALP15 in DPPC

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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Lab: 303 Engel Hall

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Re: [gmx-users] POPC: Fatal error:

[shakira shukoor]

Hi
The error states that the number of POPC molecules in your configuration
file and that mentioned in your topology files are not same. The number
refers to the total number of atoms.

On Wed, Apr 29, 2020 at 6:20 PM Dutta, Kunal  wrote:

> Dear Friends,
> I'm trying to learn Tutorial 2: KALP15 in DPPC
> 
> 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
> ---
> "
>
> Thank you for your kind help.
> Sincerely,
> Kunal
>
> --
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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