VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Wed Apr 10 2013 - 10:41:17 CDT

Thank you Josh,

I have also realized that I really need to align all molecules before
converting to PDBs however, I cannot find a command for doing this. I
wrote a log file "log align.log" while I aligned the molecules over the
trajectory for a smaller dcd file. However when I look in the log file it
only says:

menu rmsdtt off
menu rmsdtt on

followed by a buch of rotate commands.

There is nothing referencing my selection (resname HEME). Do you know how
to do the alignment in a script?

I'm sorry for asking so many questinos. I know some python scripting but
tcl is new to me.

-Yarrow

> I was writing by memory and didn't actually test the code first
> (whoops). The reason my implementation only writes one frame is because
> I goofed the syntax for the animate delete call, and it dies after
> writing the first pdb. The script should read:
>
> mol new test.psf
> set nowater [atomselect top "not water"]
> 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 *all*
> }
> exit
>
> That'll teach me from not looking up syntax first. :(
> -Josh
>
> On 04/09/2013 07:50 PM, Yarrow Madrona wrote:
>> 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