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hernanchavezthielemann / GRO2LAM

Gromacs to Lammps simulation converter
MIT License
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Atoms, Bonds, etc missing in the generated data file #26

Closed l454025801 closed 4 years ago

l454025801 commented 4 years ago

Describe the bug Information about Atoms, Bonds, Angels, etc. is missing in the generated data.gro2lam file.

To Reproduce Steps to reproduce the behavior:

  1. Select gro, top, forcefield, bonded, nonbonded files
  2. Choose Atom type 'full'
  3. Click 'Convert'

Expected behavior A data file containing all info should be generated.

Screenshots

Screenshot from 2020-02-17 10-35-08

Desktop (please complete the following information): Python 3

Try to isolate the issue ;)

hernanchavezthielemann commented 4 years ago

Hi Yang,

Thanks for your feedback. Would be great to have more info about your data files, like bond- angle- kind.

However, I have to point that GRO2LAM is a python 2.7 program.

Nevertheless, if it is running and generating some output, I would say that you have to use the "autoload" function, because, with the current input something is missing.

Best regards, Hernan

l454025801 commented 4 years ago

Hello!

I have tried as you suggested but problems still occurs.

  1. I ran GRO2LAM in python2.7 environment but the same error occurred (info about atom, bond, etc,. missing).

  2. I tried the autoload function but it gave me errors. Screenshot are attached. I have checked topology file, the sequence is consistent with .gro file. According to the error info, it seems something wrong with the water topology, but I cannot figure it out.

  3. For the input files, the types are: bond -- func 1 constraint -- func 2 angel -- func 5 (Urey-Bradley) dihedral -- func 9 (proper dihedral (multiple)) & func 2 (improper dihedral)

    Error info

    Screenshot from 2020-02-18 09-33-20

    Top file

    Screenshot from 2020-02-18 09-32-50 Screenshot from 2020-02-18 09-33-09

hernanchavezthielemann commented 4 years ago

Hi Yang,

Considering the screenshots, I would say that the problem comes from your "gro" file. Because in your "top" you have a molecule named SOL, with a residue called SOL, which is the default for water. However, in your "gro" you name that water residue as HOH.

So changing HOH tag in your "gro" by SOL should make it.

Best, Hernan

l454025801 commented 4 years ago

Hi!

Sorry to trouble again. The warning says missing coefficients about HC. Since it did not mention any other atom, I am assuming there are something missing about HC in atom definition. I checked the [atomtypes] in the nonbonded.itp. Everything seems right.

Screenshot from 2020-02-13 14-56-46 Screenshot from 2020-02-18 16-21-35 Screenshot from 2020-02-18 16-22-25

Thank you !!

hernanchavezthielemann commented 4 years ago

I think that is better if you upload a test case of your files here. Then I can check.

hernanchavezthielemann commented 4 years ago

Yang? @l454025801

l454025801 commented 4 years ago

Hi Hernan,

Sorry that I haven been busy and didn't check replies for a while. Attached is the files. Appreciate for your patience and help!

Thank you T298.zip

hernanchavezthielemann commented 4 years ago

Hi Yang,

I have checked your files, and what comes out is that there are some dihedrals and impropers missing in your bonded coefficients. Now, I have added extra verbose in that error, so you can check with the new version of GRO2LAM which parameters are missing in your input data.

Best, Hernan

hernanchavezthielemann commented 4 years ago

Hi @l454025801

Please let me know if you solve the problem.

Best, Hernan

l454025801 commented 4 years ago

Hi Hernan,

Sorry that I have decided to use other software instead of lammps since I am doing all atom simulation.

Thanks Yang