VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Wed Dec 27 2006 - 20:57:25 CST

Hi,

On 12/27/06, Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar> wrote:
> Indeed this line was extracted from a pdb written by vmd, as pointed out
> before, with the command
>
> $selover writepdb $lseg.pdb

I'm not sure I'm understanding you - are you saying that the
misformatted resid came from VMD? If so, could you tell me which
version of VMD you were using? Current versions of VMD appear to work
as I've described.

Cheers,
Justin

>
> Regards
> Cesar
>
> Justin Gullingsrud escribió:
> > Hi,
> >
> > On 12/26/06, Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar> wrote:
> >> Hi Marcos,
> >> I have already tried that. What I get is
> >> atomselect set: 0 data items doesn't match 4 selected atoms.
> >>
> >> the problem with psfgen seems to be related to resid. For example
> >>
> >> ATOM 15806 SOD SOD X 2399 217.106 26.565 -44.457 1.00
> >> 0.00 M12
> >>
> >> is interpreted as resid 239 by psfgen during segment generation. So when
> >> it tries to read the coordinates you get
> >
> > This pdb line is misformatted: the resid should start one column to
> > the left of where it actually does. VMD (and psfgen) strictly follow
> > the pdb file format, which specifies exactly which columns each data
> > field is expected to occupy.
> >>
> >> Warning: failed to set coordinate for atom SOD SOD:239 M12
> >>
> >>
> >> What I have done is a perl command to remove the X and add a space after
> >> the resid number
> >>
> >> perl -pi -w -e 's/X(\s+\d+)/$1 /g;' *.pdb
> >
> > Your script has the effect of not only removing the X (which is
> > irrelevant to the problem, as Marcos pointed out), but also shifting
> > the resid one column to the left, which causes the resid to be read
> > the way you wanted to.
> >
> > Cheers,
> > Justin
> >
> >>
> >> Regards
> >> Cesar
> >>
> >>
> >> Marcos Sotomayor escribió:
> >> >
> >> > Hi Cesar,
> >> >
> >> > What about trying something like $selover set chain " " before writing
> >> > the pdb files?
> >> >
> >> > In any case, pdb files written by vmd should work fine with psfgen,
> >> > even if they have a chain identifier X... what error did you get when
> >> > using coordpdb?
> >> >
> >> > Marcos
> >> >
> >> > On Tue, 26 Dec 2006, Cesar Luis Avila wrote:
> >> >
> >> >> Dear all,
> >> >> I want to split a pdb into several segments for later use with
> >> >> psfgen. The problem that I am facing is that for each segment that I
> >> >> write into a new pdb, I get an additional X in the chain column. In
> >> >> the original pdb there were no chain identifiers. This results on a
> >> >> problem when reading the coordinates from the new pdb with coordpdb
> >> >> in psfgen.
> >> >>
> >> >> This is the script that I use to split the pdb
> >> >>
> >> >> set all [atomselect top all]
> >> >> set lseglist [lsort -unique [$all get segid]]
> >> >> foreach lseg $lseglist {
> >> >> set selover [atomselect top "segid $lseg"]
> >> >> $selover writepdb $lseg.pdb
> >> >> }
> >> >>
> >> >> A line from the original PDB file
> >> >>
> >> >> ATOM 26852 CLA CLA 2 31.223 -0.301 20.128 1.00
> >> >> 0.00 BCL
> >> >>
> >> >> The same line in the final PDB. Note that the chain identifier was
> >> >> added by vmd.
> >> >>
> >> >> ATOM 1 CLA CLA X 2 31.223 -0.301 20.128 1.00
> >> >> 0.00 BCL How may I instruct VMD to write pdb without chain
> >> >> identifier?
> >> >> Regards
> >> >> Cesar
> >> >>
> >> >
> >>
> >>
> >>
> >
> >
>
> 

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