normal initram.sh error

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11 months 1 day ago #7512 by BioSFLab
BioSFLab created the topic: initram.sh error
Hi folks,
we are doing CG simulations on protein alone following Martini_proteins protocols with gmx 5.1.2. The simulations worked great, however we have problem in converting some of our favorite frames back to all atom model. When executing a initram.sh script we get the following error:


Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 2902)

we would greatly appreciate your suggestions,
Cheers,
www.svedruziclab.com

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11 months 14 hours ago #7517 by peterkroon
peterkroon replied the topic: initram.sh error
Hi,

please provide the exact command you used, and the full output it gave.

Peter

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10 months 4 weeks ago - 10 months 4 weeks ago #7523 by BioSFLab
BioSFLab replied the topic: initram.sh error
I used the command ./initram.sh -f frame388.pdb -p gsekb.top -o frame388aa.gro -to charmm36

frame388.pdb is a frame taken from a coarse grained trajectory that consists only of a protein (without solvent and ions) and gsekb.top is a topology file I used when I was making a CG simulation. I deleted water and solvent molecules in a .top file. The full error it gives me is:

Program gmx grompp, VERSION 5.1.2
Source code file: /home/iodorcic/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 605

Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
does not match topology (backmapped.top, 2902)

The notes are: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
And the second: System has non-zero total charge: -6.000000
Total charge should normally be an integer.

The file 0-backward.gro is made, but the only thing that is written in it is the following:

Backmapped structure from MARTINI to charmm36
0
26.61030 26.61030 26.61030 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

backmapped.top file is the same as the input .top file and the backmapped.ndx file is empty.
I tried to run the same command, but with the .pdb file from a trajectory that has both solvent and ions with the protein, but then this happens:

./initram.sh -f frame388.pdb -p gsek.top -o frame388aa.gro -to charmm36

Checking dependencies:
backward.py ... /home/zsvedruzic/gsek_coarsegrain/backward.py
gmx ... /opt/gromacs-5.1.2/bin/gmx
/home/zsvedruzic/gsek_coarsegrain/backward.py -f frame388.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p gsek.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36
Traceback (most recent call last):
File "/home/zsvedruzic/gsek_coarsegrain/backward.py", line 644, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/zsvedruzic/gsek_coarsegrain/backward.py", line 318, in __init__
self.atoms = [pdbAtom(i,strict) for i in lines if isPDBAtom(i) or rest.append(i)]
File "/home/zsvedruzic/gsek_coarsegrain/backward.py", line 251, in pdbAtom
return (str(a[12:16]),str(a[17:21]),int(a[22:26]),a[21],float(a[30:38])/10,float(a[38:46])/10,float(a[46:54])/10)
ValueError: invalid literal for int() with base 10: '271a'

I probably missed a step somewhere, but have no idea where.
Last Edit: 10 months 4 weeks ago by BioSFLab. Reason: .

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10 months 4 weeks ago #7524 by riccardo
riccardo replied the topic: initram.sh error

BioSFLab wrote: I used the command ./initram.sh -f frame388.pdb -p gsekb.top -o frame388aa.gro -to charmm36

frame388.pdb is a frame taken from a coarse grained trajectory that consists only of a protein (without solvent and ions) and gsekb.top is a topology file I used when I was making a CG simulation. I deleted water and solvent molecules in a .top file. .


If I read this correctly, you're using a CG top file. Note that the top passed to the script must be the target atomistic topology.

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10 months 3 weeks ago #7532 by BioSFLab
BioSFLab replied the topic: initram.sh error
It worked, thank you very much!

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