VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
Date: Sun Jun 23 2013 - 09:34:10 CDT

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.

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?

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

> 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?

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?