VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jun 23 2013 - 09:08:14 CDT

On Sun, Jun 23, 2013 at 3:08 PM, leila karami <karami.leila1_at_gmail.com> wrote:
> Dear VMD users
>
>
> I loaded 2 gro files (bilayer membrane and drug). I inserted drug into
> bilayer membrane using (Move -> Molecule).
>
> Now, I want to have 1 gro file (containing bilayer membrane and drug).
>
> 1) How to do this? How to save 2 gro file in 1 gro file?

with a text editor? ;-)

>
> 2) Is my manner correct for insertion of the drug into bilayer membrane?

no. how do you handle overlapping atoms?

> 3) Is there another way for insertion of the drug into bilayer membrane?

there are whole tutorials on that. merging the .gro files is usually
the minor tasks. you also need to adjust the corresponding topology
information.

if you need a quick-n-dirty method to just merge the files and resolve
overlaps, you can try this.
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal

topotools requires that you knows what you are doing, so i recommend
you spend some time reading the documentation (also of VMD).

axel.

>
> Any help will highly appreciated.
>
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.