AMBER Archive (2004)

Subject: AMBER: Amber

Date: Tue Sep 28 2004 - 14:28:32 CDT

('binary' encoding is not supported, stored as-is) Hello, Amber:

I am still blocked here. Can anyone helps me out? I have been trying to
change different formate for the atoms, such as 84.ND2. But none of them
work. According to the manual, the command should be: name mask1 mask2.
How exactly the mask be specified? It is so hard for people like me with
little knowing on unix. Could I suggest that the Amber turoials include
some examples of the commonly used commands?

And I would like to measure the total energy levels from the trajectoies.
Could anyone tell me how exactly is the input file for ptraj?

I try to measure the distance between the two atoms. One is ND2 at
 residue 84. The other is O at residue 197. I use the command which you
 correct for me in my file. But still have some problem. This is
 what I got:

PTRAJ: distance out model1-3-md1-dist1.dist time 0.1 :84_at_ND2 :197_at_O
WARNING: Error in mask string, no "@" or ":" present (model1-3-md1-dist1.dist)
 Mask [:84_at_ND2] represents 1 atoms
Segmentation fault (core dumped)


Please help.


> ==============Original message text===============
> On Mon, 27 Sep 2004 20:48:11 GMT "Thomas E. Cheatham, III" wrote:
> > trajin model1-3-md1.crd
> > distance first out model1-3-md1-dist1.dist 84_at_ND2 197_at_O time 0.1
> > strip :WAT
> > go
> This is not a proper atom selection, I assume you want residue 84?
> distance out model1-3-md1-dist1.dist time 0.1 :84_at_ND2 :197_at_O
> The command summary should print out a summary stating what atoms were
> picked. If it does not, increase the verbosity level (prnlev 3).
> -----------------------------------------------------------------------

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to