VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Dec 27 2006 - 12:54:25 CST

Indeed this line was extracted from a pdb written by vmd, as pointed out
before, with the command

$selover writepdb $lseg.pdb

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
>> >>
>> >
>>
>>
>>
>
>