[lammps-users] lammps2pdb tool

Dear all

I intend to create pdb file from atoms dump file. for this aim I have used lammps2pdb tool but it works incomplete.
when I used “perl lammps2pdb.pl solvate” then I saw :

lammps2pdb v2.2.5 ©2007

Info: creating atom ids
Info: creating bonds
Info: creating PSF index
Info: writing positions for timestep 12

this created the following pdb that is incomplete because my system has 84 atoms.

REMARK
REMARK solvate_trj.pdb GENERATED FROM solvate_ctrl.psf AND solvate.dump
REMARK CREATED BY lammps2pdb v2.2.5 ON Mon Aug 23 15:16:37 IRDT 2010
REMARK
CRYST1 9.324 9.757 9.802 90 90 90 P 1 1
ATOM 1 OH2 TIP 1 2.75 8.844 9.629 1.00 0.00 WT1
ATOM 2 1 2.11 8.29 9.998 1.00 0.00
ATOM 3 1 2.164 9.245 8.962 1.00 0.00
ATOM 4 H1 TIP 1 1.661 6.681 1.943 1.00 0.00 WT1
ATOM 5 1 1.943 5.739 1.981 1.00 0.00
ATOM 6 1 0.778 6.599 1.483 1.00 0.00
ATOM 7 H2 TIP 1 4.618 8.125 7.777 1.00 0.00 WT1
ATOM 8 1 5.405 7.919 8.314 1.00 0.00
ATOM 9 1 4.002 8.458 8.422 1.00 0.00
ATOM 10 OH2 TIP 2 3.403 4.687 9.815 1.00 0.00 WT1
ATOM 11 2 3.109 5.272 9.097 1.00 0.00
ATOM 12 2 3.817 3.973 9.327 1.00 0.00
ATOM 13 H1 TIP 2 2.71 6.185 7.54 1.00 0.00 WT1
ATOM 14 2 2.467 6.236 6.561 1.00 0.00
ATOM 15 2 3.41 6.855 7.58 1.00 0.00
ATOM 16 H2 TIP 2 3.32 1.439 3.693 1.00 0.00 WT1
ATOM 17 2 3.018 1.263 2.795 1.00 0.00
ATOM 18 2 4.218 1.737 3.533 1.00 0.00
ATOM 19 OH2 TIP 3 4.539 2.605 8.295 1.00 0.00 WT1
ATOM 20 3 5.46 2.702 8.123 1.00 0.00
ATOM 21 3 4.434 1.616 8.363 1.00 0.00
ATOM 22 H1 TIP 3 4.654 5.717 5.023 1.00 0.00 WT1
ATOM 23 3 5.059 5.126 4.395 1.00 0.00
ATOM 24 3 5.409 5.785 5.634 1.00 0.00
ATOM 25 H2 TIP 3 3.686 8.353 3.40100 1.00 0.00 WT1
ATOM 26 3 4.494 7.93 3.084 1.00 0.00
ATOM 27 3 3.041 7.727 3.197 1.00 0.00
ATOM 28 OH2 TIP 4 5.45 9.067 5.337 1.00 0.00 WT1
ATOM 29 4 4.722 8.84 4.711 1.00 0.00
ATOM 30 4 4.939 8.77 6.117 1.00 0.00
ATOM 31 H1 TIP 4 2.421 3.775 5.058 1.00 0.00 WT1
ATOM 32 4 2.684 2.934 4.652 1.00 0.00
ATOM 33 4 3.219 4.34 5.048 1.00 0.00
ATOM 34 H2 TIP 4 5.141 1.611 0.499 1.00 0.00 WT1
ATOM 35 4 4.697 1.11 1.234 1.00 0.00
ATOM 36 4 6.031 1.302 0.586 1.00 0.00
ATOM 37 OH2 TIP 5 5.461 6.754 1.943 1.00 0.00 WT1
ATOM 38 5 6.412 6.627 2.018 1.00 0.00
ATOM 39 5 5.209 5.956 1.434 1.00 0.00
ATOM 40 H1 TIP 5 7.314 0.228 9.152 1.00 0.00 WT1
ATOM 41 5 7.447 0.196 8.15700 1.00 0.00
ATOM 42 5 8.219 0.336 9.426 1.00 0.00
ATOM 43 H2 TIP 5 7.529 4.508 1.396 1.00 0.00 WT1
ATOM 44 5 8.313 4.582 0.857 1.00 0.00
ATOM 45 5 6.783 4.511 0.768 1.00 0.00
ATOM 46 OH2 TIP 6 7.881 3.518 5.7 1.00 0.00 WT1
ATOM 47 6 8.55 4.225 5.812 1.00 0.00
ATOM 48 6 7.07 3.834 6.169 1.00 0.00
ATOM 49 H1 TIP 6 9.016 4.086 8.814 1.00 0.00 WT1
ATOM 50 6 9.377 5.001 8.813 1.00 0.00
ATOM 51 6 8.726 3.741 9.661 1.00 0.00
ATOM 52 H2 TIP

Please Help.

Regards
Mari

I'll let Paul answer this one.

Steve

I'm not sure what the problem is on this. Pieter in't Veld is the author, and he's agreed to have a look at it later this week. Might help if you could send one snapshot from your dump file.

Paul

Hi Paul

Here it is.

Thanks in advance
Mari

solvate.dump (3.24 KB)

solvate_trj.pdb (4.08 KB)

Dear Paul

I had used lammps2pdb from 27Aug09 in above and was incomplete. Now, when I used lammps2pdb from 17Jul10 it was true and I succeed.

Thanks
Mari