These Python scripts were written originally by Keir Novik, but he can no longer support them. See some documentation at the top of the files - they are supposed to be fairly self-explanatory.

amber2lammps.py converts AMBER files into LAMMPS input format dump2trj.py converts LAMMPS dump files into AMBER format dump2try99.py same as dump2trj for LAMMPS 99 format

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Modifications in file amber2lammps.py, by Vikas Varshney Dated July 5, 2005 Email address : vv5@uakron.edu

Lines 222-226: Undid the shifting of the atoms in the periodic box. LAMMPS is going to take care of it by image atoms. Make sure that when you dump the coordinates by LAMMPS to view in VMD, print them in the format mentioned in the dump2ptraj.py section later.

Lines 378-391: Added an if statement to see whether .crd or .top file is being read. This if statement helps in assigning the title if the title is not present in the files.

Line 394: Added an if statement, not to read lines which start with % in the topology file.

Lines 430-432: Changed if statement condition to read the current simulation time from .crd file. I put the remainder condition instead of equal to condition. The simulation time adds one value to the length of the Item_list, so remainder condition can be applied easily to see if simulation time data is present in the .crd file or not.

In general, the initial .crd files dont have simulation time information while restart files do have them.

Some other minor additions:

I added few lines to print the names which are being read currently. This helps in seeing current state of the programs which are listed below

Lines 382, 389, 420, 428, 436, 490, 498, 550, 555, 560, 565, 570, 575, 580, 595, 600, 610, 615, 620, 631, 636, 648, 657, 666, 677, 688, 701, 720, 725, 730, 735, 740, 745, 750, 755, 767, 769, 771, 778, 785, 806, 821, 897.

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Modifications in file dump2trj.py, by Vikas Varshney Dated July 5, 2005 Email address: vv5@uakron.edu

First, the atoms should be dumped in the following format.

dump group-ID custom N tag type xs ys zs ix iy iz

Modifications:

Lines 117-119: I modified the lines to get the actual co-ordinates instead of box coordinates. If we dont do that and try to see the file in vmd, we observe long bond lengths of the molecules whose one part is on one side of periodic box and the other part is on other side of periodic box.

Lines 239 & 244: Changed x to mdcrd.

Once you do that. Open the original topology file in VMD (with parm7) and then mdcrd file (crdbox) to see the time evaluation of the problem.

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Example input script, by Paul Crozier 1 Sept 2005

Here is an example of a typical LAMMPS input script for use with a data file built by amber2lammps.py:

units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style harmonic dihedral_style harmonic pair_style lj/cut/coul/long 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.yourdata fix 1 all nve special_bonds amber thermo 1 thermo_style multi timestep 0.5 run 2