From: Leyla Celik (lc_at_chem.au.dk)
Date: Mon Feb 14 2005 - 09:44:53 CST
Hi,
I am not all that efficient at NAMD yes... What is "nedit" and how do I use it?
/Leyla
Citat Gianluca Interlandi <gianluca_at_bioc.unizh.ch>:
> 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
> -----------------------------------------------------
>
-- Leyla Celik Ph.d. student Department of Chemistry University of Aarhus Langelandsgade 140 DK-8000 Aarhus C Denmark Tel: +45 8942 3869 e-mail: lc_at_chem.au.dk
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