VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jun 23 2013 - 12:22:58 CDT

On Sun, Jun 23, 2013 at 4:34 PM, leila karami <karami.leila1_at_gmail.com> wrote:
> Dear Axel
>
> Very thanks for your reply.
>
>
>> 1) How to do this? How to save 2 gro file in 1 gro file?
>
>>> with a text editor? ;-)
>
> If I use a text editor, final gro file gives a undesirable coordinate. I
> want to put drug exactly
> in water phase of balayer membrane.

of course you do this *after* you have adjusted the coordinates. doing
it before doesn't make any sense.

> My purpose of this question is that If I load 2 gro files in VMD
> simultaneously, How to save a new gro file of those?

you cannot. it has been explained many, many times. different files
are loaded into VMD as different entities called molecules in
"vmd-lingo". that is why you have scripts, either based on psfgen or
topotools, that merge both "molecules" into a third, combined molecule
that you can then save.

>> 2) Is my manner correct for insertion of the drug into bilayer membrane?
>
>>> no. how do you handle overlapping atoms?
>
> 1) My drug is almost small.

if you have a dense system, you *do* have overlap.

2) I put drug in water phase of balayer
> membrane. Thus there is not overlapping atoms problem.

there will be, or your system has a hole already. neither is good.

>
>> 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.
>
>
> I have not problem about topology information. My main problem is to save 2
> gro files loaded in VMD as 1 gro file?

you will have it.

> When I load 2 gro files in VMD, save coordinates item is inactive. My
> purpose of this question is that If I load 2
> gro files in VMD simultaneously, How to save a new gro file of those?

if you had spent some time reading the documentation and the link i
pointed out, instead of repeating what you already wrote before, you
would have what you wanted.

axel. 

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