Search found 6 matches

by denniej0
Wed Mar 11, 2009 7:55 pm
Forum: Visualization
Topic: Visualization of the membrane
Replies: 4
Views: 8198

Re: Visualization of the membrane

To use the script, open the tcl window and do the following commands: source GBSWmemb GBSWmemb <tmemb value> <msw value> the hydrophobic core value and interface value should use the same values that you'd use for GBIM or GBSW in charmm code. For example, if you had a 35 tmemb (core) value and 2.5 m...
by denniej0
Wed Mar 11, 2009 7:49 pm
Forum: Visualization
Topic: Visualization of the membrane
Replies: 4
Views: 8198

Re: Visualization of the membrane

The simplest ways to "view" an implicit bilayer in VMD is to use the draw commands or create a pdb file with points and then do a trace of those. Below is a quick tcl script for the VMD to draw an implicit bilayer. If any errors occur just rename GBSWmemb to a command not used in VMD and that should...
by denniej0
Fri Oct 10, 2008 6:47 pm
Forum: Feature requests
Topic: Error message request
Replies: 0
Views: 6479

Error message request

This program is super! There is only one small feature request that I think might benefit new users. If we could have an error message appear when the syntax isn't correct for the 'mode' command that would be great. I was using the manual's syntax for: 'mode Transrot scan' and couldn't figure out wh...
by denniej0
Thu Oct 09, 2008 5:05 am
Forum: Bugs
Topic: Novice assistance
Replies: 6
Views: 10496

Re: Novice assistance

Many thanks Martin and Jakob.

The issue was definitely the CPU and CPU flags. I installed a new CPU with SSE2 on the Linux computer and now executing hippo is no longer an issue!

Many thanks again!
by denniej0
Wed Oct 08, 2008 2:00 pm
Forum: Bugs
Topic: Novice assistance
Replies: 6
Views: 10496

Re: Novice assistance

I used the standard input file that came with the program first but I still got the same error. When that happened I decided to take a minimalist approach and put only a few commands in the script. It's good to know that in the future I can't do that. The CPU's that I'm working with are: vendor_id :...
by denniej0
Mon Oct 06, 2008 9:17 pm
Forum: Bugs
Topic: Novice assistance
Replies: 6
Views: 10496

Novice assistance

This is probably a stupid problem so please bear with me as I'm a novice when it comes to Hippo. I downloaded both the Windows and Linux version of Hippo and am having difficulty running the executable file. I get the same error for both versions "Illegal instruction". I'm not sure what this means. ...