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Add ability to write CHARMM coordinate files. #739

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drroe merged 7 commits into from
Jul 12, 2019
Merged

Add ability to write CHARMM coordinate files. #739

drroe merged 7 commits into from
Jul 12, 2019

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@drroe
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@drroe drroe commented Jul 11, 2019

Previously, could only read.

  [help Formats trajout cor]
    Write options for Charmm COOR: Keywords: cor; Extensions: '.cor'
	keepext                : Keep filename extension; write '<name>.<num>.<ext>'
	ext                    : Use 'extended' format (default when > 99999 atoms).
	segid <segid>          : Use <segid> as segment ID for all atoms.
	segmask <mask> <segid> : Use <segid> as segment ID for atoms selected by <mask>.

@drroe drroe self-assigned this Jul 11, 2019
@drroe drroe merged commit 13f551f into Amber-MD:master Jul 12, 2019
@drroe drroe deleted the charmmcorwrite branch July 12, 2019 12:14
@Olllom
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Olllom commented Dec 5, 2019

This is super helpful, Dan. Thanks!
A minor suggestion: writing out the periodic box vectors in the header comment could be a good idea. Only if it is not too much work of course.

@hainm
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hainm commented Dec 5, 2019

A minor suggestion: writing out the periodic box vectors in the header comment could be a good idea.

@Olllom Just curious: why is that helpful?

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Olllom commented Dec 5, 2019 via email

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drroe commented Dec 6, 2019

writing out the periodic box vectors in the header comment could be a good idea.

It's not a problem. Can you give an example of the format you would prefer?

@Olllom
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Olllom commented Dec 7, 2019

Here's an example of what openmm writes into the pdb header:

REMARK   1 CREATED WITH OPENMM 7.3, 2019-02-28
CRYST1   30.584   30.584   30.584  90.00  90.00  90.00 P 1           1

Maybe that would work.

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