Subject: a question about design charge distribution in charmm

From: wei <[email-masked]>
Date: Thu, 15 May 2003 10:12:16 -0400

Dear Rick:

I need to do a simulation of a molecule which has an azobenzene group ( -phe-N=N-phe-),I need to set the partial charge for this group, I did a QM calculation with
B3LYP/6-311G(d) for the azobenzene in vacuum and get the charges, now the question is can I use it directly in rtf file, as I remember, the charges in charmm are 
always smaller than reality, is it right? if I can not use it, what should I do? 

wei

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From: Rick Venable <[email-masked]>
Date: Thu, 15 May 2003 17:47:09 -0400

I've been making molecular animations from CHARMM trajectories in MPEG1
format using mpeg_encode* for a while, but I'm having trouble finding
good MPEG1 players for M$ Windows and MacOS these days.  The only 2 that
were decent were VMPEG for M$, and Sparkle on the Mac; in particular,
they allow the user to set the frame rate for playback.  However, these
haven't been updated in some time; I don't think there's a native OSX
version of Sparkle, for instance.

    * from a series of still frames rendered via POV-Ray

In contrast, newer apps either don't play MPEG1 at all (M$ Media Player,
for instance) and others will play the MPEG1 files, but offer no means
of controlling the frame rate (QuickTime, RealPlayer).  My questions
are:

Are there other inexpensive or free media players for M$ and Mac that
can handle MPEG1 and can provide a way to set the playback speed?

Can anyone recommend other inexpensive animation software for making
"movies" in a common format from a series of still frames?

Is anyone aware of conversion tools, that might convert MPEG1 to
QuickTime or other common format?

I prefer Linux tools, but I'll use whatever works.  Thanks.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
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"Don't blame me, I voted for Kang."
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