From: Sindu (sindu_at_serc.res.in)
Date: Fri Apr 26 2013 - 01:22:46 CDT
Hi Norman Geist,Could you explain step by step how to move the monomer to certain distance. Now I have two monomers at the same position.
Regards,
B.S.Sindu
On 04/26/13, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
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> 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 polymer.
>
> 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Sindu
>
> Gesendet: Freitag, 26. April 2013 06:48
>
> An: namd-l_at_ks.uiuc.edu
>
> 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.
>
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> -With regards,
>
>
> B.S.Sindu
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