AMBER Archive (2006)

Subject: Re: AMBER: RMS (fwd)

From: Wen Li (liw_at_wadsworth.org)
Date: Tue Apr 04 2006 - 10:02:02 CDT

Actually, when I tried 100 separated readin (trajin mypdb1.pdb trajin
mypdb2.pdb ...), I only got one output file which I guess is for the
result of the first trajin.

Wen

From: Wen Li <liw_at_wadsworth.org>
To: amber_at_scripps.edu
Subject: Re: AMBER: RMS

Thanks for Dr. Simmerling's help. I have the following two questions:

1. I understand that snapshots from a trajectory can be selected by
defining a time interval. However, if somehow I have snapshots in PDB
format, say 100 pdb files, should I read in these PDB by using 100 times
of trajin: trajin mypdb1.pdb, trajin mypdb2.pdb .... or put them in one
PDB file using "TER" to separate each snapshot?

If the 100 pdb files have to be read in separately:
trajin mypdb1.pdb
trajin mypdb2.pdb
...

What is the maximum number of pdb files that can be read in?

2. Would the following procedure produce what I expect to get: align
nucleotides 1-10 in 100 pdb files to a reference pdb, and calculate rmsd
of nucleotides 50-60 when nucleotides 1-10 are aligned:

trajin mypdb1.pdb
trajin mypdb2.pdb
...
reference ref.pdb
rms reference :1-10
rms reference out outputfile :50-60 nofit
go

Thanks!
Wen

On Mon, 3 Apr 2006, carlos wrote:

> I'm not sure what nts are, but in ptraj you can use
> the rms command and say "nofit" at the end. this will
> leave the structure at the previous fit. so, do a regular
> rms command fitting to 1-10, then do rms for 50-60 with nofit
> at the end of the line.
>
> Wen Li wrote:
> > I was hoping someone could help me on the following question:
> >
> > I have one molecule (100 nts) in 100 conformaions so in 100 pdb files. How
> > can I find rmsd of nts 50-60 of each conformation relative to nts 50-60 in
> > reference conformation when every conformation is aligned to the reference
> > at nts 1-10.
> >
> > Thanks,
> > Wen
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