VMD-L Mailing List

From: Jerry Ebalunode (jebalunode_at_adrik.bchs.uh.edu)
Date: Fri Mar 12 2004 - 07:11:43 CST

Hi John,
Currently VMD runs the MSMS calculation using the socketPort option. So if
the system is properly set to allow any user or program to open this port
(in the case of VMD port No. 1357) then your calculation would proceed
successfully and you can enjoy the fruit of Dr. Sanners work. However if
your system ports are not set to allow usage by MSMS, you cannot
render the MSMS surface. I have experienced this problems with two linux
machines that I set up to use DHCP for getting there ip addresses. The
first one I fixed by opening port manually using firestarter (an iptables
firewall generation gui application). For the second one I couldn't
get away with this trick. The next possible route is to set the machine to
use a static IP address, since all linux machines that have static IP
addrs., which I have installed vmd and msms runs msms calculation via vmd
calls without any problems.
Berore I do that, I have the following question regarding this issue"

Can you set vmd to run msms without using the socketport option? If yes,
how can this be done?

Can do know of any other method to make port 1357 available for msms?

Though this last question is not related, is it possible to incorporate
the ability to clip seperate objects (i.e., you rendered a molecular
surface of your protein in one representation and renderd a certain
residues in cpk or licorice, however you want to just clip only the
surface to a certain extent such that all the residues you are displaying
as well as the rest of the surface could be seen simultaneously) into vmd
design. Probably someone already asked about adding feature this before,
but I need to let the VMD developing team what my additional needs are.
Thanks for you reply in advance.

Cheers,

Jerry Ebalunode
Graduate Research Assistant
Dept. Biology and Biochemistry
University of Houston
Houston, Texas.