VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 05 2015 - 07:20:27 CDT

On Tue, May 5, 2015 at 3:13 AM, Daniel Möller
<daniel.moeller3_at_uni-greifswald.de> wrote:
> Hi,
>
> there is a simple method:
> - load your pdb as a "new molecule" as much you need for the final
> - move every molecule with "Mouse -> Move -> Molecule" to another position
> - save the new position "File -> Save coordinate" in a new file (or a temp-file)
> - copy-paste every structure in one pdb via a text editor, but between every molecule should be a "TER"
> (pay attention to the empty space at the end of the lines in your pdbs, so you don't corrupt your pdb-structure. See Ivans link for standard pdb format)

you can avoid the text editor step by using the topotools
package/plugin which is included in VMD.

https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-mergemols-list-of-molecule-ids-

axel.

>
> I hope this helps
>
> Sincerely
>
> Daniel Möller
>
> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Ivan Gregoretti
> Gesendet: Dienstag, 5. Mai 2015 05:55
> An: 丁晗
> Cc: vmd-l
> Betreff: Re: vmd-l: How to create an aggregation of molecules with VMD?
>
> Hello dingh09,
>
> Yes, multiple molecules are common in a single PDB files.
>
> For example, see the antibody structure 4NZU:
> http://www.rcsb.org/pdb/files/4NZU.pdb
>
> In that file, "CHAIN: L" is the light chain poly-peptide and the
> "CHAIN: H" is the heavy chain poly-peptide.
>
> Likewise, any co-crystal structure implies at least two molecules. The are plenty of co-crystals at RCSB.
>
> A solvated structure is yet another example of multiple molecules in a single PDB file. Granted that water is a small molecule but it is still a molecule. ;)
>
> For more on the PDB standard, see
> http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER
> In particular, look for section COMPND and look at the first and second examples.
>
> I hope this helps.
>
> Ivan
>
>
>
>
>
>
>
>
> On Mon, May 4, 2015 at 11:12 PM, 丁晗 <dingh09_at_163.com> wrote:
>> Hi,
>> I want to create an aggregation of benzene with VMD, so that I can
>> solvate them in water box and monitor the solvation process. However,
>> I can create only one molecule with molefacture. So is there any way
>> to create multiple molecules in one pdb file?
>> thank you!
>>
>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.