AW: Build polymer from monomer

From: Norman Geist (
Date: Fri Apr 26 2013 - 01:07:13 CDT

Hi Sindu,


depending on how often you plan to build polymers of different lenght, you
can do it by hand in VMD, or try to write a script for it. We usually use
scripts for such things. I guess the easiest way would be a tcl script to be
executed within the vmd console. I think the main problem you are facing, is
to position the monomers to each other properly, the bonding shouldn't be a
problem right? My initial idea is a script that works the following:


1. Ask the user how many monomers should be connected to build a

2. Load a monomer from pdb (it should be prepared to be aligned to any
axis. The best choice could be parallel to X around Y and Z)

3. Load another monomer from pdb and remember the count of the
monomers loaded.

4. As they would have the same position now, measure the X dimensions
of the molecule and move the latest monomer by that distance(+1 or2A
maybe)*count in X direction.

5. Goto 3. until you reached the target count from 1.

6. Write all the molecules to a pdb.


If it is not possible to load them all into the same molecule in VMD, simply
load them into individual molecules and cat together the pdb in the end. You
can use the molid to address the right objects then.


Maybe someone else already know a program that can do such operations, so
you would save a lot of work. Let us know if you need further help.


Good luck.


Norman Geist.


Von: [] Im Auftrag
von Sindu
Gesendet: Freitag, 26. April 2013 06:48
Betreff: namd-l: Build polymer from monomer


Dear all,

I am new to NAMD. I am trying to generate an epoxy polymer. I have created a
monomer now. From this I want to create a polymer chain.

It would be helpful if you help me in explaining how to make copies of this
monomer and to connect it to form a polymer.

Thanks in advance.



-With regards,



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