Re: Analysis of NAMD output with CHARMM

From: Gianluca Interlandi (gianluca_at_bioc.unizh.ch)
Date: Mon Feb 14 2005 - 08:07:49 CST

Hi Nathalie,

It seems that CHARMM doesn't read the residue number correctly:

> ** WARNING ** For atom in coordinate file, could not find residue in PSF,
> and
>is thus ignored:
>
> SEGID=WT1 RESID=000 RESNAME= TIP3 TYPE= H1
> *** LEVEL 1 WARNING *** BOMLEV IS -3

I mean "RESID=000" in the fifth line above points out that the columns in
the pdb are somehow shifted, exaclty as you mention in your last e-mail.
You can use "nedit" to move the columns to the place where they should be.
However, to avoid that nedit replaces empty spaces with tabs you must
select Preferences -> Tabs and unselect "Use tab characters in padding and
emulated tabs".

There must be a more elegant way, but maybe this can help you.

Best, Gianluca

----------------------------------------------------
Gianluca Interlandi gianluca_at_bioc.unizh.ch
                    +41 (0) 1 635 55 93
                    +41 (0)79 655 73 35
                    http://biocroma.unizh.ch/gianluca/

PhD-Student of the Department of Biochemistry
at the University of Zurich Irchel, Switzerland
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