normal Error during Reverse Transformation

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11 years 7 months ago #1077 by think_beyond
Error during Reverse Transformation was created by think_beyond
Hello Colleagues,

I am very new here. I have been doing the tutorials available in Martini website.

I am doing the 'protein in water' tutorial. I have converted my protein and solvent to cg system using martinize.py and did rest of the steps in the tutorial. At the end, I liked to convert the system back to fg. The tutorial on Reverse Transformation has helped me to install a modified version of Gromacs which provides the g_cg2fg program. But while using the g_cg2fg command with necessary options I have received an error 'Segmentation fault (core dumped)'
I have also referred other discussions in this forum related to the errors in Reverse Transformation but didn't help. All the discussions were about transforming the system with bilayers. How do I transform my cg system (protein in water) to fg?

Peterson J

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11 years 7 months ago #1079 by djurre
Replied by djurre on topic Error during Reverse Transformation
Getting g_fg2cg to produce something useful is indeed not always easy, but we need a bit more information here. Are you actually doing the protein described in the tutorial? Did you manage to generate a proper [ mapping ]? (At the bottom of your atomistic .itp or .top file.) Did you create the atomistic and coarse grained topology from the same pdb file?

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11 years 7 months ago #1082 by think_beyond
Replied by think_beyond on topic Error during Reverse Transformation
I have just checked my .top and .itp files and couldn't find anything called [ mapping ]. But I'm sure I've followed the tutorial carefully and nothing was mentioned in the tutorial about [ mapping ].

Yes, I am doing the tutorial with the tutorial files given in the webpage.

Can you guide me how can I get this in my .top and .itp files?

Thanks

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11 years 7 months ago #1083 by djurre
Replied by djurre on topic Error during Reverse Transformation
Something must be going wrong. I just checked the files that are online. In the fg.top file there IS a [ mapping ].

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11 years 7 months ago #1084 by think_beyond
Replied by think_beyond on topic Error during Reverse Transformation
I have got the fg.top file but had issues using it. when I issue the following command
$ g_fg2cg -pfg fg.top -n 0 -c traj.xtc -o fg.gro

Receive an error like this

"calling cpp...
Segmentation fault (core dumped)"

I also have another question, the fg.top file has information about bilayer also. I have removed the line "DPPC 128" in [ molecules ] part. Should I use this fg.top file to transform non-membrane protein system too?

Thanks

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11 years 7 months ago #1085 by djurre
Replied by djurre on topic Error during Reverse Transformation
g_fg2cg needs a FG and a cg topology. In your command the "-pcg cg.top" is missing. And if you are using the files from the tutorial, why would you remove the DPPC line? There are DPPC's in the system.

You are specifying a traj.xtc as input and a gro as output. Are you sure that is what you want? It might be more useful to give the confout.gro as an input file.

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11 years 7 months ago #1086 by think_beyond
Replied by think_beyond on topic Error during Reverse Transformation
The command I have provided was one of the possible combinations I tried after seeing errors.
I have also tried the following but turned the same errors.
$ g_fg2cg -pfg fg.top -pcg system.top -n 0 -c solvated_md.gro -o fg.gro

I am working with the files from protein in water tutorial. They dont have any DPPC at all. I am trying to convert the protein (1UBQ.pdb after simulation) in water to fg.

Thanks

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11 years 7 months ago #1087 by djurre
Replied by djurre on topic Error during Reverse Transformation
You're right, if you're using the 1UBQ files there is no bilayer indeed. In that case you can remove the line about DPPC. There also won't be a [mapping] section. You can use the version of pdb2gmx that comes with the reverse transformation gromacs version to get one: "pdb2gmx -f 1UBQ.pdb" and choose one of the forcefields that have mapping ("with MAPPING", either gromos 43a3 or gromos 53A6).

I do think the comment you just gave:

g_fg2cg -pfg fg.top -pcg system.top -n 0 -c solvated_md.gro -o fg.gro

should work with the new topology.

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11 years 7 months ago #1089 by think_beyond
Replied by think_beyond on topic Error during Reverse Transformation
Thanks for that information and I am doing the tutorial again from the scratch.

Now I have a problem during em step. It runs only for very short time and not really converging well.
the following is the final message,

Steepest Descents:
Tolerance (Fmax) = 2.00000e+03
Number of steps = 10000
Step= 0, Dmax= 1.0e-03 nm, Epot= 3.15917e+17 Fmax= 0.00000e+00, atom= 0
writing lowest energy coordinates.

Back Off! I just backed up em.trr to ./#em.trr.7#

Back Off! I just backed up em.gro to ./#em.gro.7#

Steepest Descents converged to Fmax < 2000 in 1 steps
Potential Energy = 3.1591714e+17
Maximum force = 0.0000000e+00 on atom 0
Norm of force = -nan

I have changed the em_tol value in the mdp file but still it doesn't change and produces the same result. Am I using a wrong mdp file?

Thanks

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11 years 7 months ago #1090 by djurre
Replied by djurre on topic Error during Reverse Transformation
If you are doing the "protein in water" tutorial from scratch, the problem with the em are in a 'normal' em of 1UBQ in water? No reverse transformation involved yet? Did you add water or is it still the vacuum step?

In case you did add water, have a look at you starting file to see if there are (lots) of overlapping waters. In my experience genbox sometimes generates boxes with lots of overlapping solvent, even if you set -vdwd 0.21. In that case try again with a slightly different boxsize.

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11 years 7 months ago #1093 by xavier
Replied by xavier on topic Error during Reverse Transformation
Djurre is right and when you are going through the tutorial and something does not work you want to go back a few steps and check that you have done them correctly. And it is often could to restart from scratch. A file can easily be modified and screw the all procedure.

Perseverance is good :))

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11 years 7 months ago #1095 by think_beyond
Replied by think_beyond on topic Error during Reverse Transformation
Thanks for your reply. I could succeed the 'protein in water tutorial' with your suggestions and comments.

But, during the reverse transformation (RT), I could succeed only until SA run. Here i have a confusion with the gro and top files that I need to use. The SA run is done with the cg.gro itself, not with the fg.gro that was generated during the g_fg2cg step?

I have two .top files (one is generated from the pdb2gmx with mapping and the second one is from martinize.py step). Which one should I use during RT step?

What are the changes do I need to make in a top file for SA run?

Peterson J

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11 years 7 months ago #1119 by xavier
Replied by xavier on topic Error during Reverse Transformation

think_beyond wrote: Thanks for your reply. I could succeed the 'protein in water tutorial' with your suggestions and comments.

But, during the reverse transformation (RT), I could succeed only until SA run. Here i have a confusion with the gro and top files that I need to use. The SA run is done with the cg.gro itself, not with the fg.gro that was generated during the g_fg2cg step?

I have two .top files (one is generated from the pdb2gmx with mapping and the second one is from martinize.py step). Which one should I use during RT step?

What are the changes do I need to make in a top file for SA run?

Peterson J


Did you find out the solutions?

It is not clear if the problems you describe are for your own system or still for the tutorial. If it is for your own system you should simply follow the same steps as in the tutorial ...

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9 years 2 weeks ago #4491 by nivedita
Replied by nivedita on topic Error during Reverse Transformation
Dear all
I am also trying to do cg simulation for protein in water. I have used gromacs 4.5.5 version. I took 1ubq to understand how cg is working. The step which i hv followed are:
martinize.py -f 1UBQ.pdb -o system.top -x 1UBQ-CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22
editconf -f 1UBQ-CG.pdb -o 1UBQ-CG.pdb -d 1.5
grompp -f minimization-vaccum.mdp -c 1UBQ-CG.pdb -p system.top -o minimization-vaccum.tpr
mdrun -deffnm minimization-vaccum -v
genbox -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -vdwd 0.21 -o system-solvated.gro
grompp -f minimization.mdp -c system-solvated.gro -p system.top -o minimization.tpr
mdrun -deffnm minimization -v
grompp -f equilibration.mdp -c minimization.gro -p system.top -o equilibration.tpr
mdrun -deffnm equilibration -v
grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr
mdrun -deffnm dynamic -v
finally i have dynamic.gro/tpr/edr/cpt/xtc files.
Now for doing reverse transformation i hv install rev_trans in other directory. after installation i hv run following steps using gromacs 3.3.1 ver.:
1) for mapping the protein i have run
pdb2gmx -f 1UBQ.pdb -o ubq.gro
Fatal error:
Atom H not found in residue 1 while adding mapping
but when i run
pdb2gmx -f 1UBQ.pdb -o ubq.gro -missing
then it will run along with a warning:
Generating angles, dihedrals and pairs...
WARNING: atom H not found in residue 1 while adding mapping
WARNING: atom O1 not found in residue 1 while adding mapping
WARNING: atom O2 not found in residue 1 while adding mapping
...
WARNING: atom H1 not found in residue 76 while adding mapping
WARNING: atom H2 not found in residue 76 while adding mapping
WARNING: atom H3 not found in residue 76 while adding mapping
WARNING: atom O not found in residue 76 while adding mapping
2)g_fg2cg -pfg topol.top -pcg system.top -n 0 -c dynamic.gro -o fg.gro -wat 1
Number of fg atoms 936
Number of cg atoms 1661
Reading frames from gro file 'Martini system from 1UBQ.pdb', 1661 atoms.
Reading frame 0 time 0.000
Water rewrited to normal representation
Then i have modified fg.mdp according to my requirement(by removing DPPC)
3)grompp -f fg.mdp -c fg.gro -p topol.top -o 1ubq_fg_sa.tpr
Fatal error:
Group FG_W not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.
In that case use the '-n' option.

My doubt is where i have to keep fg_w.itp? and which step is wroung?

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8 years 9 months ago #4586 by nivedita
Replied by nivedita on topic Error during Reverse Transformation
Dear all,
I have one query regarding reverse transformation. I have run CG simulation on gromacs 3.3.1 ver and than i am able to do rev-trans .
Is it possible to perform CG simulation on gromacs 4.5.5. and if yes than what are those modification i have to do to get rev-trans? because for rev-trans i need Gromacs 3.3.1 ver.

Thanks and regards

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8 years 9 months ago - 8 years 9 months ago #4587 by Clement
Replied by Clement on topic Error during Reverse Transformation
No. The method hasn't been implemented in later version of Gromacs. Use backward.py instead.
Last edit: 8 years 9 months ago by Clement.

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8 years 8 months ago #4680 by nivedita
Replied by nivedita on topic Error during Reverse Transformation
Thanks clement for your reply
My question is about backmapping.
After backmapping the structure which i got is backmapped.gro. i converted this structure in pdb file and i have performed following steps:
pdb2gmx -f backmapped.pdb -o map.gro -p topol.top -water spc
editconf
genbox
grompp minimization
than equilibartion NVT (Simulated annealing)
NPT
final production run for 20ns.
Is these steps are correct for getting good secondary structure or i have missed something.
Plz tell me if im wrong bcoz my protein having 3000 residues so im afraid to run 20ns aa-simulation.

Thanks and regards

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