normal martinze adds one more atom to the .itp chain than the *.pdb structure posses

  • tfischb
  • tfischb's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
4 months 4 days ago #7717 by tfischb
tfischb created the topic: martinze adds one more atom to the .itp chain than the *.pdb structure posses
Hello,

currently I'm working on my Bachelor-thesis. One goal I should achieve is building a Protein-Membrane with the Martini force field in order to investigate its mechanical abilities and structural stability.

For some other force fields (Amber99) I already built up the membrane and its totally fine. Now I want to martinize the membrane.

Martini v2.2
-martinze didn't throw an error
-gmx grompp:

Fatal error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: '; NGNGNVCPPGLFSNPQCC'

Martini v3.3
-martinize throw an error code:

Traceback (most recent call last):
File "/usr/lib64/python2.7/runpy.py", line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "./martinize/__main__.py", line 10, in <module>
File "./martinize/martinize/cli.py", line 204, in main
File "./martinize/martinize/core.py", line 564, in main
File "./martinize/martinize/core.py", line 35, in iter_resource
AttributeError: __exit__

-gmx grompp:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with

My first Idea to solve this problem was to start with a single protein structure, martinize it and built the membrane out of it. However this didn't work either.

Martini 2.2:
-martinize works perfectly fine
-Energy minimization with grompp:

Fatal error:
number of coordinates in coordinate file (conf+box_center.pdb, 816)
does not match topology (topol.top, 817)

Martini 3.0:
-martinize throws the same exit-Error as before
-Fatal error:
number of coordinates in coordinate file (conf+box_center.pdb, 822)
does not match topology (topol.top, 823)

The last days I was searching for the additional Atom, but so far I only know that it could be 1 of 327 SC1 Atoms.

Do you have any idea how to solve this problem or how to deal with it? I appreciate every tips and ideas to solve my problem.

Kind regards,
Tobias Fischbach

Please Log in or Create an account to join the conversation.

More
4 months 3 days ago #7719 by bart
bart replied the topic: martinze adds one more atom to the .itp chain than the *.pdb structure posses
Heya,

I can understand that this answer might feel unsatisfying, but if you need to build a CG membrane, i would just build it from scratch using insane. The configurational exploration of the all atoms simulations is so tiny that it is neglectable and it really gives you now gain in accuracy or comparability.

With that in my mind I would say don't fix the error and don't try to understand it for now. Sometimes you have to pick your battles.

Please Log in or Create an account to join the conversation.

  • tfischb
  • tfischb's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
4 months 3 days ago #7720 by tfischb
tfischb replied the topic: martinze adds one more atom to the .itp chain than the *.pdb structure posses
Hi,

thank you for your advise. After a week of search we somehow solved the Problem. I'll share my experience with you for any users who maybe encounter the same problem.

There is a bug in the current DSSP we are using because it thinks that every last VAL loop in my Protein incomplete (we cross checked it: its not) and thus it confuses martinize. However, we couldn't understand whats the Problem is, but we added the missing loop by hand and transmitted it via a string for martinize. Now it works like charm, except we don't know the problem which confuses DSSP.

Thank you for your trouble.

Please Log in or Create an account to join the conversation.

Time to create page: 0.182 seconds