VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Thu Apr 11 2013 - 08:33:14 CDT

Thanks Brian,

When you say, "load smaller psf and dcd files into vmd" you mean in the
command line right? After I used catdcd and removed the waters the DCD
file was still to large (about 5 GIGS) to load into the GUI. I guess then
you would put everything into one script and run in from the command line?

-Yarrow

> Hello,
> These are the steps that will get you the quickest results until the caver
> folks have native DCD import functionality (which they said might come
> this year).
>
> First, use catdcd to remove the water molecules from the original DCD
> files. You will need to make an index file and new psf file for the
> reduced number of atoms. Just load the original psf, and one frame from
> the original DCD file.
>
> Second, load the new smaller psf and dcd files into vmd all at once.
>
> Third align the molecule with the attached script
>
> Fourth, write out individual pdbs from this realigned trajectory that is
> already loaded into the vmd session.
>
>
> Usage:
> align 0 0 "name CA"
> This will align all the frames to the first structure of the first
> trajectory.
>
> No need for the gui interface.
>
> proc align { rmolid smolid2 seltext } {
> set ref [atomselect $rmolid $seltext frame 0]
> set sel [atomselect $smolid2 $seltext]
> set all [atomselect $smolid2 all]
> set n [molinfo $smolid2 get numframes]
>
> for { set i 1 } { $i < $n } { incr i } {
> $sel frame $i
> $all frame $i
> $all move [measure fit $sel $ref]
> }
> $ref delete
> $all delete
> $sel delete
> return
> }
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of Yarrow Madrona
> Sent: Wednesday, April 10, 2013 8:41 AM
> To: Josh Vermaas
> Cc: Yarrow Madrona; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: how to convert dcd AND ALIGN molecules then to pdbs in
> command line
>
> Thank you Josh,
>
> I have also realized that I really need to align all molecules before
> converting to PDBs however, I cannot find a command for doing this. I
> wrote a log file "log align.log" while I aligned the molecules over the
> trajectory for a smaller dcd file. However when I look in the log file it
> only says:
>
> menu rmsdtt off
> menu rmsdtt on
>
> followed by a buch of rotate commands.
>
> There is nothing referencing my selection (resname HEME). Do you know how
> to do the alignment in a script?
>
> I'm sorry for asking so many questinos. I know some python scripting but
> tcl is new to me.
>
> -Yarrow
>
>
>> I was writing by memory and didn't actually test the code first
>> (whoops). The reason my implementation only writes one frame is
>> because I goofed the syntax for the animate delete call, and it dies
>> after writing the first pdb. The script should read:
>>
>> mol new test.psf
>> set nowater [atomselect top "not water"] for {set i 0} {$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
>
>
>
> 

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