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cepid-cces / hpccs

The High Performance Collision Cross Section (HPCCS) is a new software for fast and accurate calculation of CCS for molecular ions. Based on the Trajectory Method (TM), HPCCS was parallelized and optimized to be an user-friendly program.
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Allow analysis of binary trajectories. #1

Open jcminerlanl opened 5 years ago

jcminerlanl commented 5 years ago

The current implementation uses the config.in file to determine how many ASCII inputs there are. This ultimately consumes a great deal of disk space when there are large sets of structures to analyze.

Is it possible to read from binary trajectories? For example, .xtc structural trajectories from GROMACS? The code would need to include code like libgmxcpp (https://github.com/wesbarnett/libgmxcpp).

Is it possible that such libraries could be incorporated to allow .xtc or similar files to be read?

lzanotto commented 5 years ago

Hi Jacob,

I am working on a next release with some improvements, this is a good idea that we decided to include on this release, as soon as I finish it I will publish here on Github.

Regards,

lzanotto commented 5 years ago

Hi Jacob,

If you can provide the small molecule or something similar, I can analyze and tell you if its possible.

Thanks

On Tue, Dec 4, 2018 at 7:57 PM Jacob Miner notifications@github.com wrote:

If I have a molecule that cannot have a .pqr, a small organic (non-peptide) molecule for instance, is there any way that hpccs can provide a CCS for such a case?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cepid-cces/hpccs/issues/1#issuecomment-444274520, or mute the thread https://github.com/notifications/unsubscribe-auth/AGu-c1iuURPnQhXquSCjJc3lS7SIENLkks5u1u_bgaJpZM4XUUzf .

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jcminerlanl commented 5 years ago

Here is an example:

HETATM 3550 C1 CLR A 402 -11.570 10.215 30.572 1.00 96.73 C
HETATM 3551 C2 CLR A 402 -11.488 10.197 29.053 1.00 96.92 C
HETATM 3552 C3 CLR A 402 -10.047 10.206 28.549 1.00 90.69 C
HETATM 3553 C4 CLR A 402 -9.306 8.990 29.106 1.00 78.41 C
HETATM 3554 C5 CLR A 402 -9.259 9.207 30.578 1.00 78.72 C
HETATM 3555 C6 CLR A 402 -8.059 9.373 31.160 1.00 75.22 C
HETATM 3556 C7 CLR A 402 -7.831 9.612 32.599 1.00 79.58 C
HETATM 3557 C8 CLR A 402 -9.054 9.223 33.425 1.00 83.80 C
HETATM 3558 C9 CLR A 402 -10.345 9.746 32.788 1.00 92.56 C
HETATM 3559 C10 CLR A 402 -10.577 9.291 31.320 1.00 90.37 C
HETATM 3560 C11 CLR A 402 -11.576 9.685 33.702 1.00 91.82 C
HETATM 3561 C12 CLR A 402 -11.327 10.220 35.095 1.00 92.06 C
HETATM 3562 C13 CLR A 402 -10.109 9.601 35.789 1.00 89.58 C
HETATM 3563 C14 CLR A 402 -8.915 9.772 34.832 1.00 81.93 C
HETATM 3564 C15 CLR A 402 -7.653 9.665 35.676 1.00 79.44 C
HETATM 3565 C16 CLR A 402 -8.088 10.124 37.061 1.00 68.69 C
HETATM 3566 C17 CLR A 402 -9.589 10.438 36.998 1.00 75.65 C
HETATM 3567 C18 CLR A 402 -10.338 8.139 36.136 1.00 93.00 C
HETATM 3568 C19 CLR A 402 -11.263 7.914 31.377 1.00 88.40 C
HETATM 3569 C20 CLR A 402 -10.268 10.205 38.341 1.00 79.56 C
HETATM 3570 C21 CLR A 402 -11.730 10.614 38.283 1.00 82.59 C
HETATM 3571 C22 CLR A 402 -9.525 10.929 39.464 1.00 80.72 C
HETATM 3572 C23 CLR A 402 -10.074 10.536 40.827 1.00 79.53 C
HETATM 3573 C24 CLR A 402 -9.016 10.668 41.904 1.00 80.54 C
HETATM 3574 C25 CLR A 402 -9.278 11.806 42.891 1.00 76.88 C
HETATM 3575 C26 CLR A 402 -9.117 11.347 44.328 1.00 56.32 C
HETATM 3576 C27 CLR A 402 -10.640 12.421 42.668 1.00 81.77 C
HETATM 3577 O1 CLR A 402 -9.959 10.185 27.129 1.00 88.45 O
HETATM 3578 C1 CLR A 403 -8.121 14.107 31.634 1.00 84.56 C
HETATM 3579 C2 CLR A 403 -8.212 14.200 30.127 1.00 83.85 C
HETATM 3580 C3 CLR A 403 -9.553 13.678 29.625 1.00 94.93 C
HETATM 3581 C4 CLR A 403 -10.749 14.338 30.331 1.00105.51 C
HETATM 3582 C5 CLR A 403 -10.581 14.440 31.815 1.00100.18 C
HETATM 3583 C6 CLR A 403 -11.607 14.116 32.631 1.00 97.65 C
HETATM 3584 C7 CLR A 403 -11.557 14.191 34.110 1.00 99.27 C
HETATM 3585 C8 CLR A 403 -10.479 15.183 34.554 1.00104.30 C
HETATM 3586 C9 CLR A 403 -9.150 14.876 33.865 1.00 99.40 C
HETATM 3587 C10 CLR A 403 -9.238 14.912 32.320 1.00 97.50 C
HETATM 3588 C11 CLR A 403 -7.985 15.697 34.416 1.00 90.37 C
HETATM 3589 C12 CLR A 403 -7.876 15.674 35.917 1.00 90.48 C
HETATM 3590 C13 CLR A 403 -9.153 16.076 36.646 1.00100.58 C
HETATM 3591 C14 CLR A 403 -10.279 15.201 36.064 1.00102.02 C
HETATM 3592 C15 CLR A 403 -11.365 15.063 37.124 1.00102.61 C
HETATM 3593 C16 CLR A 403 -10.628 15.326 38.440 1.00105.07 C
HETATM 3594 C17 CLR A 403 -9.138 15.576 38.126 1.00101.88 C
HETATM 3595 C18 CLR A 403 -9.481 17.556 36.506 1.00 97.70 C
HETATM 3596 C19 CLR A 403 -9.038 16.385 31.917 1.00101.23 C
HETATM 3597 C20 CLR A 403 -8.409 16.443 39.168 1.00 97.19 C
HETATM 3598 C21 CLR A 403 -6.952 16.709 38.822 1.00 98.69 C
HETATM 3599 C22 CLR A 403 -8.467 15.822 40.553 1.00 98.40 C
HETATM 3600 C23 CLR A 403 -8.822 16.838 41.622 1.00 93.67 C
HETATM 3601 C24 CLR A 403 -8.633 16.202 42.985 1.00 90.76 C
HETATM 3602 C25 CLR A 403 -7.737 17.025 43.907 1.00 83.37 C
HETATM 3603 C26 CLR A 403 -6.271 16.716 43.664 1.00 71.48 C
HETATM 3604 C27 CLR A 403 -8.126 16.804 45.356 1.00 74.85 C
HETATM 3605 O1 CLR A 403 -9.707 13.958 28.237 1.00 85.27 O

lzanotto commented 5 years ago

Jacob,

Do you have the file extension or description of each column?

jcminerlanl commented 5 years ago

This is a .pdb file: 'ATOM/HETATM' 'atom number' 'atom name' 'resid name' 'chain ID' 'resid num' 'X' 'Y' 'Z' 'Occ' 'B-value' 'atom'

lzanotto commented 5 years ago

Hi Jacob, Since it is a PDB file, did you try to follow this instruction? • Making the PQR File PDB2PQR is a Python software package that provides a utility for converting protein files in PDB format to PQR format. For more information about PDB2PQR tool you can visit: http://pdb2pqr.sourceforge.net/.

H++ is a server that given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. For more information about H++ server see: http://biophysics.cs.vt.edu/.