VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Apr 11 2013 - 10:08:08 CDT

Yes the commandline would work just fine for loading the reduced set of coordinates. How much memory do you have on this system?

regardless, of memory size, you can use catdcd to cut the dcd in as many pieces as you want.
You would use separate catdcd commands to read in the first half of the full dcd file and then the second half.

The alignment would require one extra step and that is you would need a pdb file of the very first structure to align the 2nd, 3rd, ... DCD files to.

brian

________________________________________
From: Yarrow Madrona [amadrona_at_uci.edu]
Sent: Thursday, April 11, 2013 6:33 AM
To: Bennion, Brian
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

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