Error: There are no atoms in the system (with write("Data Atoms") command) about moltemplate HOT 4 CLOSED

I try to build an entire big system instead of build the single monomer. I don't know why, but it works now.

from moltemplate.

Hi Zoe
If you send me all of the moltemplate (.LT) files you are using I will have a look. Please also tell me what command you were using to invoke moltemplate.sh. For example:

moltemplate.sh monomer.txt

If this is how you were invoking moltemplate.sh, then it will not work because the "monomer.txt" file does not contain any "new" commands. When you invoke moltemplate.sh, it should probably look like this instead:

moltemplate.sh system.lt

The "system.lt" file contains "new" commands to make copies of one or more PDMS polymers.
There is typically a file named "polymer.lt" (or "PDMS.lt", or something similar) which defines what a PDMS polymer is. It will contain "new" commands which make copies of the monomer you defined in "monomer.txt".
For examples of this approach, please see:

1. https://moltemplate.org/examples.html#butane
2. https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_COMPASS/butane#butane-example
3. https://moltemplate.org/doc/moltemplate_manual.pdf#section.6
   (Chapter 6 is only 2 pages long.)

Anyway, if you send me files you are confused about, I will have a look.

from moltemplate.

Hi Dr. Jewett,

Thank you for the hint!
I thought the command write ("Data Atoms") is the one creates the items, so I can create monomer alone by run the monomer.lt files. But I now realize I should run the script that contain the "new" command, i.e., polymer.lt in my case.

Thank you for really kind suggestions!

from moltemplate.

I'm glad this helped!
If it's okay, I will close this issue now.

from moltemplate.