VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Tue Dec 26 2006 - 15:03:23 CST

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
>