How to get Lammps data file for multiple proteins of same type

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1

Dear Everyone,

I have one question regarding getting Lammps data file for many proteins of the same kind.

I got one protein from Protein Data Bank (it is known that the atom number limitation of pdb file is 99999). I got the Lammps data file for one protein, no problem here.

But if I want to get Lammps data file for 13 proteins of same kind, just with the atoms’ coordinates changed. I am not sure how to deal with it: I cannot merge 13 proteins in one pdb file due to the number limitation.

Can anyone give me some advice here?

Thanks a lot!

Lili

2

I think the replicate command is what you are looking for.

Carlos

3

As long as you're happy with 13 in a line, this will do the job (damn those prime numbers...)
Otherwise, you could write a little script to read the data file, and replicate the protein atoms at suitable offsets.

4

VMD switches to hexadecimal numbers at that point. So if you happen to
use VMD's psfgen and charmm2lammps to make your box, the 99999 atoms
and 9999 residues are actually not a limitation.

Sebastian.

Dear Everyone,

I have one question regarding getting Lammps data file for many
proteins of the same kind.

I got one protein from Protein Data Bank (it is known that the
atom number limitation of pdb file is 99999). I got the Lammps data
file for one protein, no problem here.

But if I want to get Lammps data file for 13 proteins of same kind,
just with the atoms' coordinates changed. I am not sure how to
deal with it: I cannot merge 13 proteins in one pdb file due to the
number limitation.

Can anyone give me some advice here?

Thanks a lot!

Lili

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Dr. Sebastian Busch
University of Oxford
Department of Biochemistry
Laboratory of Molecular Biophysics
South Parks Road, Oxford, OX1 3QU, UK
+44 1865 61 33 11
[email protected]...
http://www2.bioch.ox.ac.uk/mclaingroup/Sebastian.html

5

Thanks All for your reply. For my 13-protein complex, each protein has its specific atoms’ coordinates (I got them by translating and rotating the original protein from the data bank).

I will check the “replicate” command to see if it can do the work.

Best,

Lili

6

Thanks All for your reply. For my 13-protein complex, each protein has its
specific atoms' coordinates (I got them by translating and rotating the
original protein from the data bank).

I will check the "replicate" command to see if it can do the work.

if you want to import the coordinates that you have computed, you can
*first* use the replicate command to build a suitable topology and
*then* use the read_dump to overwrite the coordinates. if you have
individual pdb files, you can combine them and simply remove the END
records and don't have to worry about it. if you have a version of
LAMMPS with the USER-MOLFILE package included, you can read the pdb
file directly, otherwise you can convert it into a supported format
(e.g. .xyz) with VMD.

axel.

7

Hi Sebastian,

Yes, I did use VMD to merge the proteins and use charmm2lammps to get the data file :slight_smile:

I did see the strange numbering after 99999 atoms, but I was not sure it was correct and can be recognized by the ch2lmp and Lammps later on to run. Great to know it is not a problem now.

Many thanks!

Lili