VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Tue Apr 09 2013 - 19:50:10 CDT

Hi Josh,

Thanks for your help. For some reason your script only writes out the
first pdb and not the rest. This is what I am using:

mol new test.psf
set nowater [atomselect top "not water"]
set nf [molinfo top get numframes]
for {set i 0} {$i < 10} {incr i} {
    animate read dcd CIN-SUM-every10.dcd beg $i end $i waitfor all
    $nowater writepdb WT_$i.pdb
    animate delete
}
exit

> Another option is to run VMD in text mode. Make a simple script
> (script.tcl) like this:
>
> mol new psffile.psf
> set nowater [atomselect top "not water"]
> for { set i 0 } { $i < 70000 } { incr i } {
> animate read dcd dcdfile.dcd beg $i end $i waitfor all
> $sel writepdb $i.pdb
> animate delete
> }
> exit
>
> This will go through each frame one by one and write it to its own pdb,
> while never keeping more than 1 frame in memory. You can then run it
> from the command line with something like:
>
> vmd -dispdev text -e script.tcl (see
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node207.html for more on
> using the command line to start vmd, including the extra step required
> on windows)
>
> -Josh
>
> On 04/09/2013 01:12 AM, peter.schmidtke_at_fr.netgrs.com wrote:
>> Hey,
>>
>> Consider using ambertools ptraj for instance, which could do the pdb
>> export.
>>
>> Best regards.
>>
>> Peter
>>
>> -----Message d'origine-----
>> De : owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] De la part
>> de Yarrow Madrona
>> Envoyé : mardi 9 avril 2013 01:43
>> À : VMD mailing list
>> Objet : Re: vmd-l: how to convert dcd to pdbs in command line
>>
>> Hello,
>>
>> I am trying to convert a dcd to a series of pdb's without opening the
>> VMD GUI. The reason is that I don't have enough ram to store the DCD
>> (70,000
>> frames) into memory. VMD always crashes unless I use a truncated DCD. I
>> would like to use all frames since the frames will be analyzed by
>> another software (Caver3.0). Is there a way to tell vmd to write out all
>> PDBs in the command line (preferably without water although I can remove
>> those later)?
>>
>> Thank you
>>
>>
>> --
>> Yarrow Madrona
>>
>> Graduate Student
>> Molecular Biology and Biochemistry Dept.
>> University of California, Irvine
>> Natural Sciences I, Rm 2403
>> Irvine, CA 92697
>>
>>
>>
>>
>
> 

-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697