I want to add missing atom from pdb file, among 8000 files using command line and set n-terminal = NH2, c-terminal = COOH. What's software that help me?
However, I using pdb2gmx from GROMACS, but I have a problem for set termini (-ter) because I can't set -ter = NH2 and COOH in command line when using loop iteration. Have you any ideas for solve this problem?
Thank you
Selections for all GROMACS programs can easily be made in loops using echo.
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
The order in the termini listing is always the same, so the selection is straightforward. The only complication is if the force field has specific termini for Gly or Pro; then the selection changes, but that can be made an if-condition in a loop.
You should try profix from Jackal package: http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal
Chimera UCSF or Modeller also may provide what you need.
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