Does pdbtools support the free version of CHARMM (version 40)?

[maoyibo]

Recently Chemistry at HARvard Macromolecular Mechanics released a free version of CHARMM, called 'charmm'. I tried to uses the free version of charmm with pdbtools to clean a pdb file, but failed. The script ./pdb_clean.py shows :
CharmmInterfaceError It appears that CHARMM has failed. Input written to: charmm.inp Output writen to: charmm.out Please tell me how can I solve this problem?

https://www.charmm.org/charmm/showcase/news/free-charmm/

[Zsailer]

To help diagnose the problem, would you mind re-running the script with a --keep_tmp flag.

This should leave you with some extra files produced by pdbtools. I want to know:

1. Does anything gets printed in the out.cor?
2. What gets printed in the charmm.out file?

Looks like the I/O interface from the free version of CHARMM is different than full CHARMM and is confusing pdbtools (since it is a simple wrapper of CHARMM). If neither of these files exist, or if charmm.out has an error message, then the input commands to CHARMM have changed. Otherwise, if charmm.out has normal content, its possible that it looks different than output from the full version of CHARMM.

Either case, the CHARMM I/O module in pdbtools will need some editing.

[maoyibo]

Dear Zachary:

I had re-runned the script, and the result files was collected in the file pdbtools_charmm_log.tgz. I hope this will help you to diagnose the problem. The charmm.tar.gz file was the free version of charmm I used.

Yours Yibo 20160410

p.s. I'm sorry to send a empty email before. ​ charmm.tar.gz https://drive.google.com/file/d/0B4DrnkE8JRflSXVaQ01vRVMyNUU/view?usp=drive_web ​

2016-04-07 4:15 GMT+08:00 Zachary Sailer notifications@github.com:

To help diagnose the problem, would you mind re-running the script with a --keep_tmp flag.

This should leave you with some extra files produced by pdbtools. I want to know:

1. Does anything gets printed in the out.cor?
2. What gets printed in the charmm.out file?

Looks like the I/O interface from the free version of CHARMM is different than full CHARMM and is confusing pdbtools (since it is a simple wrapper of CHARMM). If neither of these files exist, or if charmm.out has an error message, than the input commands to CHARMM have changed. Otherwise, if charmm.out has normal content, its possible that it looks different than output from the full version of CHARMM.

Either case, the CHARMM I/O module in pdbtools will need some editing.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/harmslab/pdbtools/issues/3#issuecomment-206540682

[alfredoq]

Deal pdbtools developers, I am also experiencing this problem with the pdb_clean.py script while using it with free CHARMM. Any solution has been reported since this post was first created? thank you very much in advance,

Alfredo

[satishramchurn]

I have uncompressed and installed free charmm under Linux/GNU However, with a test input like:

• CHARMM test script

• date ! This will print the date and time stop

charmm is not producing any output.

Grateful for help on this one.