Re: AMBER: rms

From: Carlos Simmerling <>
Date: Wed, 16 Feb 2005 08:59:43 -0500

I said I do NOT think it is CM motion removal. This is described in the
manual (NSCM). I think it is possible that it is imaging of your 2 chains.
Please view all of the structures, not just first and last. It is important
to know what your molecule is doing, not just to read values output by
a program. If it is imaging, this is not a "big problem" as you say but it
is normal. Please check the iwrap section of the manual and also read about
the image command in ptraj.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Gustavo Pierdominici Sottile wrote:

> Hi,
> I have already written about the problem with the rms and I was
> asked if I have a duplex. The answer is yes. the system is composed of
> two polipeptide chains and 6000 water molecules. The number of atoms
> is 30000. You told me that the problem could be the removel of the CM
> motion. What does it mean? I havenīt seen the dynamics but the first
> and the last structure look nice. It would be strange there exists a
> big problem in the middle
> Thanks in advance
> Gustavo

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 16 2005 - 14:53:00 PST
Custom Search