VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Sun Apr 13 2014 - 07:28:33 CDT

Dear Josh, Dear all,

Thanks for the tip .. I did manage to get "measure fit" to superimpose
exactly what I want using the "order" parameter.
Now, the fit is performed correctly but if I try to measure the rmsd
using "measure rmsd" this still re-orders the atoms even when I use the
correct list of indices as a selection. Unfortunately, "measure rmsd"
does not accept the order parameter input either ... Is there any trick
to fix this ? Or do I simply need to write a new procedure that
calculates the rmsd atom by atom ?

Best wishes
Vlad

On 04/12/2014 04:37 PM, Josh Vermaas wrote:
> Hi Ashish,
> You should try to include the list in your replies. I don't use
> LAMMPS, so I have no idea what its output structure is (for instance,
> I have no idea how topology is stored).
>
> Your output looks like a simple xyz formatted file. This is enough to
> make a PDB, since neither file format stores connectivity information.
> Step 1 is to load the output into VMD (mol new file.xyz). When reading
> in xyz files, VMD assumes that the first column is the atom name (and
> in this case will do the conversion from 1->H and 2->He). From there
> you can make atomselections to rename things and write a pdb.
>
> set Cusel [atomselect top "name H"]
> $Cusel set name Cu
> set Zrsel [atomselect top "name He"]
> $Zrsel set name Zr
> set all [atomselect top "all"]
> $all writepdb output.pdb
>
> Quick question, are there really spaces between minus signs and the
> z-coordinate in your files? If so, that's something you'll need to
> correct. :)
> Good luck!
> -Josh Vermaas
>
> On 04/12/2014 09:12 AM, Ashish .Chauniyal wrote:
>> Hi Josh,
>> Thanks for helping out before. However I am still a little stuck with
>> things that are too trivial for experts like you. Here is my complete
>> problem, I have a box consisting of several thousand atoms namely Cu
>> and Zr. These atoms are simulated using LAMMPS under specific
>> conditions. This information about the atoms and their coordinates is
>> saved in a data file, which I was hoping to read in VMD. I have to
>> merge this structure with another similar structure at some
>> interface. There fore I need to do operations such as displacing the
>> entire atoms by some value and then combining things.
>>
>> So with this in mind ,I was using topotools but really got confused
>> since all the documentation emphasis is on molecular structures and
>> all that. I feel my case is simple , read some file, move it around
>> and then merge it for future use in lammps.
>> The last bit of code I sent you was modified from Alex Kohlemeyrs
>> tutorials, but it does not really work in may case. I have a lammps
>> data file in the following format.
>> 6400
>> Atoms. Timestep: 300
>> 2 -41.9649 84.4817 4.01756
>> 2 -40.6413 -83.3137 -3.67139
>> 1 -42.2923 -84.0662 -1.43588
>> 1 42.1149 -82.3104 -1.12892
>> 2 -39.1661 84.087 - 3.9539
>> 1 -36.989 -83.8449 -4.08889
>> 1 -34.7283 85.2272 - 0.185181
>> 2 -38.7322 -84.3027 - 1.5362
>> 1 -33.5458 84.8172 -4.30221
>> 2 -31.8768 -83.9025 4.09117
>>
>> where 1 and 2 denote atom type Cu and Zr respectively and the other 3
>> colums represent x y & z. How do you think I can play with this in
>> VMD. Also the documentation on this is very hard to find.
>> Thanks again.
>>
>> regards,
>> Ashish
>>
>>
>> On Fri, Apr 11, 2014 at 8:59 PM, Josh Vermaas <vermaas2_at_illinois.edu
>> <mailto:vermaas2_at_illinois.edu>> wrote:
>>
>> Hi Ashish,
>>
>> If you are just trying to make a pdb-formatted file out of this,
>> literally all you need to do is:
>>
>> set all [atomselect top "all"]
>> $all writepdb filename.pdb
>>
>> I'm not familiar with the file format you are using. What do the
>> first two columns and last three columns mean? What does VMD
>> think the fields mean (ie, if you go to the graphical
>> representations window, what are the values associated with each
>> keyword)? You haven't given me (or anyone else) enough
>> information to help you effectively. My advice would be to play
>> around with the graphical representations, and try to play around
>> with the atomselections to separate the two types of atoms. The
>> easiest way to do this would probably be to look at the
>> keyword-value pairs (under the "selections" tab of the graphical
>> representations window), and determine which keywords/values pick
>> between Copper and not copper atoms.
>>
>> Good luck!
>> -Josh Vermaas
>>
>>
>> On 04/11/2014 10:17 AM, Ashish .Chauniyal wrote:
>>> Dear Josh,
>>> I was having some problem with the usage of the 'atomselect'
>>> command and wonder if you could suggest something as you in your
>>> previous post. I am a little confused with the explaination
>>> given in the user guide regarding atomselect.
>>>
>>> I have a file containing 2 types of atoms and their coordinates.
>>> given below <Atomid> <type><x><y><z>.
>>>
>>> Atoms
>>>
>>> 4003 2 -3.6948671457303270e+01 -8.2178357941409985e+01
>>> -1.0333348401063144e+01 0 0 1
>>> 807 1 -3.6990060733492541e+01 -8.0262837680770645e+01
>>> -8.2698926717344481e+00 0 0 0
>>> 1 1 -4.1360378365219930e+01 -8.0595341475920435e+01
>>> -1.1523945200048335e+01 0 0 0
>>> 85 2 -3.8964145243144991e+01 -7.9837065660776460e+01
>>> -1.0375438044916475e+01 0 0 0
>>> ........
>>>
>>>
>>> I just need to read the file an make a .pdb format out of it.
>>>
>>> ## this is part of the code, where i try to read only type 1
>>> atoms, is this correct?
>>> set selc [atomselect top "resid 1"]
>>> $selc set type Cu
>>> $selc set resname PPP
>>>
>>> set resid {}
>>> foreach r [$selc get residue] {
>>> incr r
>>> lappend resid $r
>>> }
>>> $selc set resid $resid
>>> $selc delete
>>>
>>>
>>> Thanks in advance,
>>>
>>> regards,
>>> Ashish Chauniyal
>>> Deptt. Mechanical Engg.
>>> BITS Pilani(INDIA)
>>>
>>>
>>> On Fri, Apr 11, 2014 at 7:58 PM, Josh Vermaas
>>> <vermaas2_at_illinois.edu <mailto:vermaas2_at_illinois.edu>> wrote:
>>>
>>> Hi Vlad,
>>>
>>> It is certainly doable, but requires some bookkeeping on
>>> your end. If you look at the user guide, the measure fit
>>> command takes an optional argument:
>>> *fit /selection1/ /selection2/ [weight /weight/] [order
>>> /index list/]*
>>> Again taken from the user guide:
>>> The optional flag /order/ takes as argument a list of
>>> 0-based indices specifying how to reorder the atoms in
>>> /selection2/ (Example: To reverse the order of atoms in a
>>> selection containing 10 atoms one would use order {9 8 7 6 5
>>> 4 3 2 1 0}).
>>>
>>> I've never needed to use this feature so far, but what I
>>> believe you'd need to do is make an index list that puts
>>> them into the order you want. This is an outline to get you
>>> started:
>>>
>>> set indexlist [list ]
>>>
>>> foreach resid [list 8 9 10] {
>>> set sel [atomselect 2 "resid $resid"]
>>> #To figure out how big the offset needs to be, we need
>>> to know how many atoms in the selection are out of order
>>> before us.
>>> set abovesel [atomselect 2 "resid 8 9 10 and resid >
>>> $resid"]
>>> set counter 0
>>> foreach el [$sel get index] {
>>> lappend indexlist [expr { [$abovesel num] +
>>> $counter] } ]
>>> incr counter
>>> }
>>> $abovesel delete
>>> $sel delete
>>> }
>>>
>>> The reason you have to do these gymnastics is because VMD
>>> stores atoms in the order they were loaded, and decides if
>>> an atom is inside or outside of an atomselection following
>>> this order. This is why if you ever tried an atomselection
>>> like "resid 11 1", it will return indices that are in
>>> increasing order, rather than returning the indices
>>> belonging to residue 11 then those belonging to residue 1.
>>>
>>> -Josh Vermaas
>>>
>>>
>>>
>>>
>>> On 04/11/2014 07:16 AM, Vlad Cojocaru wrote:
>>>> Dear all,
>>>>
>>>> I have a rather simple question but for which I did no
>>>> figure an answer yet ... I have 2 DNA molecules which I
>>>> want to superimpose.
>>>> The superposition should be done like this:
>>>>
>>>> res 1 from mol 1 on res 10 from mol 2,
>>>> res 2 from mol 1 on res 9 from mol 2,
>>>> res 3 from mol 1 on res 8 from mol2,
>>>>
>>>> .. and so on ...
>>>>
>>>> If I do the selections "resid 1 to 3" and "resid 10 to 8",
>>>> it does not work as VMD tries to superimpose 1 on 8, 2 on
>>>> 9, and 3 on 10.
>>>> I also tried to change the residue numbers in mol 2 such as
>>>> res 10 becomes res 100, res 9 becomes res 101, res 8
>>>> becomes res 102 (to have ascending order). However, still
>>>> no success, VMD does not care about the residue number, it
>>>> still tries the same. ...
>>>>
>>>> Do I need to change all atom indices to actually make VMD
>>>> superimpose the way I want ? Or is there an easier solution
>>>> to this ?
>>>>
>>>> Thanks for any advice ..
>>>>
>>>> Best wishes
>>>> Vlad
>>>>
>>>>
>>>
>>>
>>
>>
> 

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de