[nursya]

 

Right from the start the output from Step6_Minimization is error. The Log6.0 recorded was:

Select_atom> Syntax error. bracket is not a preliminary rank_no =0

Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted

mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do was:

Process name: [[3839,1],0]
Exit code: 1

For your information i run tutorial for POPC, Minimization(6.0) and rst file can be found, and Log6.0 show success to be proceed to Step6.1

But for my problem is, the LPS membrane bilayer cannot create the step6.0 rst file at all thus also error for step6.1

Hope for your attention

Nur

[jwjung]

Okay. The error message says that there is a mistake in writing atom selections. Could you read manual carefully how to write atom selection in the control input?

[nursya]

Dear Jwjung,

This is how i do it..

^{export OMP_NUM_THREADS=1}

mpirun -np 1 home/ubuntu/Downloads/genesis-1.4.0/bin/spdyn step6.0_minimization.inp > log6.0

As from charmm-gui, i chose no of lipid: LPS upperleaflet 7 lowerleaflet 7. At first i am suspecting the size of LPS could be too big, innitially did tried 22 upper and 22 lower before decreasing it to 7.

then i chose 0.25M CaCl2, genesis, genesis, 303.15 and monte carlo

Perhaps the ‘language’ input created by charmm-gui for LPS cannot be read by Genesis-1.4.0?

[jwjung]

I guess the size of LPS is not a problem. I think the problem is just incorrect writing in [SELECTION] sections in your control input step6.0_minimization.inp. Didn’t you change anything in the control input from the one generated by charmm-gui?

[nursya]

i did not change anything from charmm-gui downloaded files.

i am suspecting the step6.0_minimization.inp files for this LPS is incomplete. because:
[SELECTION]
group1 = sid:MEMB and ((rnam: and ()) or (rnam: ECLIPA and (an:PA)))

remember the error notes that i wrote in Log6.0 is:
Select_atam> Syntax error. brakcet slis empty rank_no = 0

while the input files that i successfully run, POPC (step6.0_minimization.inp) that site read:
[SELECTION]
group1 =sid:MEMB and ((rnam:POPC and (an:P)))

differences you can see now is there is empty space in the bracket for inp file LPS(step6.0_minimization)

I tried to find what that script is, maybe ECR3O55 but still error after i fill that in (ECR3O55: e.coli R3, o55) as ECLIPA is the resname for e.coli type 1 Lipid A.

Hope for your help to figure this things out

[jwjung]

I guess you can write

group1 = sid:MEMB and (rnam:ECLIPA and (an:PA))

in the control input.

[nursya]

Hi

Tried that before, the error state:
Setup_Enefunc_Rest_Group> no atom in group rank_no = 1
Setup_Enefunc_Rest_Group> no atom in group rank_no = 0

Guess need to fill in that empty bracket resname also..

ECLIPA is E.coli lipid a type 1.
Another 2 parts of E. coli LPS need to mentioned I think, the core and the o-antigen. Mine is LPS type 1, R3, O55. But I dont know the resname for this R3 and O55..

[jwjung]

The error message means that there is no such a atom in your input. I don’t know your input, so it’s difficult to say, but you need to check your pdb or psf. Please check the residue name or atom name in your pdb or psf.

[nursya]

good news. they already fixed the bugs(charmm-gui developer). i notice the new one resname was just: (rnam:ECLIPA and (an:PA)). they removed sid:MEMB and those empty bracket.

thanks for this nice discussion Dr Jung! i appreciate it