VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Jul 06 2015 - 22:57:49 CDT

Thank you Norman. This is the code used and it worked fine.

proc trace1 {n} {
set i 0
set input [open "myout.dat" r]
set atomid [read $input]
set mol [mol new ../setup/wat_spce.psf type psf waitfor all]
for {set frm 0} {$frm < $n} {incr frm} {
mol addfile ../run01/wat_run01.dcd type dcd first $frm last $frm waitfor
all molid $mol
set select [atomselect $mol "index $atomid" frame 0]
$select writepdb out$i.pdb
set i [expr $i+1]
animate delete beg 0 $mol
$select delete
}
}

Then I merged the pdbs using the command you mentioned.

Thanks again.

Regards,
Monika

On Mon, Jul 6, 2015 at 3:28 PM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> You forgot to delete the frame again to save memory.
>
> You have to include the $frm within the pdb filename and merge the pdbs
> afterwards.
>
>
>
> Do you get any error?
>
> How do you call the proc?
>
>
>
> Norman Geist.
>
>
>
> *From:* Monika Madhavi [mailto:monikamadhavi_at_gmail.com]
> *Sent:* Monday, July 06, 2015 11:02 AM
> *To:* Norman Geist
> *Cc:* VMD Mailing List
>
> *Subject:* Re: vmd-l: How to write coordinates to a pdb without replacing
> existing entries
>
>
>
> Thank you for your suggestion.
>
> I loaded the initial frame using mol new and mol addfile and extracted the
> indexes of the atoms needed. I write their indexes into a separate dat file
> called "myout.dat"
> Then I wrote another script as shown below.
> However, the pdb does not generate. Can you please suggest where I am
> going wrong?
>
> proc trace1 {n} {
> set numfr $n
> set input [open "myout.dat" r]
> set atomid [read $input]
> set mol [mol new ../setup/wat_spce.psf type psf waitfor all]
> for {set frm 0} {$frm < $n} {incr frm} {
> mol addfile ../run01/wat_run01.dcd type dcd first $frm last $frm waitfor
> all molid $mol
> set select [atomselect $mol "index $atomid"]
> $select frame $frm
> animate write pdb traced.pdb 0 end [expr $n-1] waitfor all sel $select $mol
> $select update
> }
> $select delete
> }
>
> Regards,
>
> Monika
>
>
>
> On Mon, Jul 6, 2015 at 12:58 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> You could write a small TCL script which loads the trajectory frame per
> frame. Most of the required commands can be obtained using VMD Main->Log
> tcl commands to console and doing them by hand so:
>
>
>
> 1. load initial structure and parameters
>
> 2. as long as there are frames
>
> a. load 1 frame
>
> b. save your structure to a individual pdb file with a increasing
> number like: mypdb1.pdb
>
> c. remove the frame from vmd
>
> d. goto a.
>
> Of course you need to have some counters to control which frame you are
> loading from the trajectory file.
>
> Afterwards you could do something like:
>
>
>
> cat $(ls -t mypdb*.pdb) > merged.pdb
>
>
>
> to combine all the pdb to a single file.
>
>
>
> Norman Geist.
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of Monika Madhavi
> Sent: Monday, July 06, 2015 6:55 AM
> To: Josh Vermaas
> Cc: Norman Geist; VMD Mailing List
> Subject: Re: vmd-l: How to write coordinates to a pdb without replacing
> existing entries
>
>
>
>
> Dear Norman,
>
> So far the script I used worked fine. Now I want to analyze a very large
> trajectory (dcd) using the same script. For small trajectories the script
> worked fine since I could load the whole trajectory at once. Now because my
> trajectory is very large (36 GB) my RAM (4 GB) cannot process it at once. I
> tried using bigdcd but, I could not get it done. Any suggestion is greatly
> appreciated.
>
> I need to select the molecules from the initial frame and then save their
> coordinates in all frames.
>
> Thank you.
>
> Regards,
>
> Monika
>
>
>
> On Thu, Mar 12, 2015 at 2:21 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
> Thanks Norman, it works perfectly!!!
>
> Monika
>
>
>
> On Mon, Mar 9, 2015 at 7:00 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
> Hi Monika,
>
> It is possible to write out a "trajectory pdb". I think, based on the
> documentation for the animate command (
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html), that it
> would be something like this:
>
> animate write pdb output.pdb beg 0 end 0 sel $sel
>
> The $sel writepdb version of file writing I believe can only handle one
> frame at a time. Also, does it need to be a pdb output? A binary format is
> going to be much smaller.
>
> -Josh Vermaas
>
> On 03/09/2015 05:26 AM, Monika Madhavi wrote:
>
> Thanks Norman, your answer is exactly what I wanted. Is it possible to loop
> this around each frame also. Can I write the pdb entries for my
> atomselection ($sel here) for each frame in the same pdb?
>
> Regards,
> Monika
>
> On Mon, Mar 9, 2015 at 3:12 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de
>
> wrote:
> This is not the way it should be done. It is much easier and faster to
> just collect the resids you need 1st and write out the coordinates
> afterwards. You can easily collect the list of resids with “lappend�.
>
>
>
> example:
>
>
>
> set myresids {}
>
> for {whatever} {
>
> if {whatever} {
>
> lappend myresids $resid
>
> }
>
> }
>
> set residlist [lrange $myresids 0 end]
>
> set sel [atomselect top “resid $residlist�]
>
> $sel writepdb my.pdb
>
> $sel delete
>
>
>
> Norman Geist.
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Monika Madhavi
> *Sent:* Monday, March 09, 2015 7:24 AM
> *To:* Joaquim Rui de Castro Rodrigues
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: How to write coordinates to a pdb without replacing
>
>
> existing entries
>
>
>
> Thanks Rui,
> Actually I can select the residue ids I want to select but they are
> selected in a random manner and the number is large. Therefore I am
> wondering whether I can write coordinates of the selected molecule at the
> time it is selected without giving the whole list of ids at the end.
>
> Regards,
> Monika
>
> Monika Madhavi
> Department of Physics
> University of Colombo
>
> On Mar 8, 2015 11:03 PM, "Monika Madhavi" <monikamadhavi_at_gmail.com> wrote:
>
> I want to achieve the result I would get if I write this command while
> looping around without writing line 2 as it is.
>
> set residlist {1 2 3 4 5}
>
> set sel [atomselect top "resid 1 2 3 4 5"]
>
> $sel writepdb out.pdb
>
> $sel delete
>
> Regards,
>
> Monik
>
>
>
>
>
> On Sun, Mar 8, 2015 at 10:47 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
> Thanks Joaquim. Actually i set N outside the loop. What i want is to write
> all the coordinates in a single pdb file. As an example, something like
>
> If my molecule is water,
>
> Resid atomname coordinates
> 1 H1 .........
> 1 H2 ........
> 1 OH .........
> 2 H1 .........
> 2 H1 ..........
> 2 OH .........
>
>
>
>
> --
>
> W.A.Monika Madhavi
>
> Lecturer (Probation),
>
> Department of Physics,
>
> University of Colombo.
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.