VMD-L Mailing List

From: Xiao-Ping Zhang (zhang_at_biokemi.su.se)
Date: Sat Mar 18 2000 - 14:00:37 CST

Dear Dr. John Stone,

Sorry, I did not answer your first question in my reply this afternoon. I
tried VMD1.4 MSMS drawing method just now for a small peptide (7 amino
residues), It works perfectly. But It did not work on a protein with 226
amino residues.

Also, I tried VMD1.5a1. On my machine (Intel pentium II 400, Redhat Linux
5.2), MSMS in VMD does not work even on the same small peptide which I
mentioned above.

Thank you for your attention.

Sincerely,

Xiao-Ping Zhang

At 09:16 AM 3/17/00 -0600, you wrote:
>
>Hi,
> Have you tried running MSMS on a small molecule to see if the
>problem is related to the size of your molecule? There is a known
>problem with the interface between VMD and MSMS that can cause it to
>fail when generating surfaces for large molecules, or on slow machines.
>We've been working on improving the VMD/MSMS interface recently, and this
>should be fixed once and for all in VMD 1.5. What kind of machine are
>you using by the way? We are planning on making the first pre-release
>version of VMD 1.5 available today. You might try this new version with
>your same MSMS 2.4.x binary and see if it works better, we have already
>made various improvements to the MSMS interface code in this pre-release
>version, but there's still more to be done before VMD 1.5 is finished.
>
>Thanks for your patience,
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Fri, Mar 17, 2000 at 02:53:22PM +0100, Xiao-Ping Zhang wrote:
>> Hi,
>>
>> I installed VMD 1.4 and MSMS 2.4 on Redhat Linux 5.2. When I draw molecule
>> in VMD with MSMS method, the msms calculation works fine (you can see from
>> vmd console window), but nothing showed up in the Graphic window. What I
>> did was putting the msms executable in /usr/local/bin/ directory. Do I need
>> to install something else?
>>
>> Thank you.
>>
>> Sincerely,
>>
>> Xiao-Ping Zhang
>>
>> ------------------------------------------------
>> Xiao-Ping Zhang
>> Department of Biochemistry
>> Stockholm University
>> 106 91 Stockholm
>> Sweden
>>
>> Phone: 46-08-162582 / 162472
>> Fax: 46-08-153679
>> e-mail: zhang_at_biokemi.su.se
>>
>>
>
>--
>
>Theoretical Biophysics Group Email: johns_at_ks.uiuc.edu
>Beckman Institute http://www.ks.uiuc.edu/~johns/
>University of Illinois Phone: (217) 244-3349
>405 N. Mathews Ave FAX: (217) 244-6078
>Urbana, IL 61801, USA Unix Is Good For You!!!

------------------------------------------------
Xiao-Ping Zhang
Department of Biochemistry
Stockholm University
106 91 Stockholm
Sweden

Phone: 46-08-162582 / 162472
Fax: 46-08-153679
e-mail: zhang_at_biokemi.su.se