error in membrane protein molecular dynamics simulation

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1

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Hi All,

I have successfully run the KALP15 peptide in DPPC layer. I have to run the molecular simulation of an ion channel in membrane.

I have run the molecular simulation of my protein into DPPC. In my protein two long loops (around 100 residues each) are missing. So, I got three itp for protein named as chainA, chainA2 and chainA3. I have applied the strong restraint on protein as well which gave me 3 strong_posre and I have mentioned them in topol.top.

Then I have inflated it by:-

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

Here, total 18 lipids i.e. 10 from upper leaflet and 8 from lowerleaflet is removed.

Then i have minimized it by:-

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

Then, I have done the shrinkage by using run_inflategro.sh

I got the following error:-

RUNNING SHRINKING ITERATION 2…

system_shrink1_em.gro does not exist. Exiting.

I am a new to membrane protein molecular dynamics. I am not able to understand the reason of this error.

I would be very thankful for suggestions to resolve this error.

Thank you in advance.

2

Some prior step failed. Run the commands interactively rather than via the script, and look for obvious fatal errors printed to the terminal (which should also be printed when using the script).

3

Thank you for your suggestions jalemkul,

I am able to do successfully run with another protein as a membrane protein MD using KALP15 peptide tutorial.
I am new to membrane protein molecular dynamics.

When I have run the:-
gmx mdrun -deffnm system_inflated_em
I got the error (Error : 1, in attached picture) ,
fatal error:
There is no domain decomposition for 15 ranks that is compatible with the given box and a minimum cell size of 7004.76 nm
change the number of ranks or mdrun option -rdd or -dds

Here i have used the one processor and run this command:-
gmx mdrun -deffnm system_inflated_em -nt 1

Although, my energy minimization is done, but i got this output (Error : 2, in attached picture)

Maximum force = inf on atom 6426
Norm of force = inf

Further, when I have run the
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

I got the error (Error : 3, in attached picture)

Invalid command-line option -s
File ‘system_shrink1_em.tpr’ does not exist or is not accessible.
The file could not be opened
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -f
File ‘system-shrink1_em.gro’ does not exist or is not accessible.
Reason: No such file or directory
(call to fopen() returned error code 2)

I would be very thankful for suggestions to resolve this error.

Thank you in advance.

Errors
Errors900×695 193 KB

4

Your molecules are probably broken. Make sure you’re making molecules whole with trjconv.

5

Thank you again for your suggestions jalemkul,

I have full protein which does not have any gap or missed residues.
What could be the reason of the breaking of molecules during molecular simulation ?

I did not understand this:-
Make sure you’re making molecules whole with trjconv .

Could you please elaborate it.

Thank you again.

6

Given your nomenclature and use of InflateGRO I assumed you were using the protocol taken from my membrane protein tutorial. Is that not the case? Molecules need to be whole, i.e. not broken across periodic boundaries. My tutorial explains this.

7

Thank you again for your suggestions jalemkul.

Yes, I am using the protocol taken from your membrane protein tutorial.

I will try again as per the instructions of your membrane tutorial.