AMBER Archive (2004)

Subject: Re: AMBER: Amber

From: Tomas Linhart (linht0am_at_karlov.mff.cuni.cz)
Date: Tue Sep 28 2004 - 14:50:28 CDT

Well, the mask format is specified in ptraj documentation, in short,
you probably want something like :84_at_ND2, which selects atom ND2 in
residue 84.

To extract energy information from the trajectory, you have to preprocess
mdout file.

On Tue, Sep 28, 2004 at 07:28:32PM +0000, bybaker_at_itsa.ucsf.edu wrote:
> 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 ptraj.in 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.
>
> Bo
>
> > ==============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).
> >
> >
> > -----------------------------------------------------------------------
>
>
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