VMD-L Mailing List

From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Fri Sep 21 2007 - 16:04:56 CDT

John,

Thanks for your comment. Unfortunately, I can't use a psf structure
because that requires some CHARMM formated files and my system is
derived from a bunch of GROMACS *.itp files. I can probably write a
quick-and-dirty script to convert topologies but I not sure a simple
residue renumbering worth it :)

Nicolas

John Stone wrote:
> Nicolas,
> You cannot presently modify the bond determination criteria on-the-fly,
> but you can interactively edit the bonds and cause VMD to re-analyze
> the structure on-the-fly. You could also use psfgen or autopsf to
> build a complete structure and load a PSF with your PDB which would
> more permanently address the issue. I plan to add some features that'll
> allow more flexible automatic bond determination criteria soon in support
> of people that work with very unusual structures that combine
> silicon nanodevices and biological molecules, that would likely
> help in cases like yours as well.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 21, 2007 at 02:14:23PM -0600, Nicolas Sapay wrote:
>
>> Thanks for the fast answer,
>>
>> I have tried the selection text "residue $res" as you have suggested but
>> the problem was still there. So, I have re-rechecked my pdb file.
>> Apparently, a bond between the O1 and the P1 of the 200the lipid is not
>> recognized by VMD. Lipid 200 is thus considered as 2 different residues.
>> Same thing probably happened to 3 other lipids. That would explain why I
>> have 4 more residues that expected. The problem is probably solvable if
>> I find a way to modify the VMD criteria that define bonds.
>>
>> Nicolas
>>
>> Axel Kohlmeyer wrote:
>>
>>> On Fri, 21 Sep 2007, Nicolas Sapay wrote:
>>>
>>>
>>> nicolas,
>>>
>>>
>>> NS> 5 set sel [ atomselect $molid "$seltext" ]
>>> NS> 6 # Retrieve the 'residue' number of the selection
>>> NS> 7 set reslist [ lsort -integer -unique [ $sel get residue ] ]
>>> NS> 8
>>> NS> 9 # Assign a new 'resid' to each residue of the selection
>>> NS> 10 foreach res $reslist {
>>> NS> 11 # Do a temporary selection
>>> NS> 12 set tmpsel [ atomselect $molid "$seltext and residue
>>> NS> $res" ]
>>>
>>> please note, that in this case you overwrite only the resids
>>> of those atoms that are in the selection, so parts of the same
>>> residue may have different resids after the procedure.
>>> if you want to overwrite the resid of all atoms in a given residue,
>>> just use the selection text of "residue $res".
>>>
>>> NS> 13 $tmpsel set resid $start
>>> NS> 14 $tmpsel delete
>>> NS> 15 # Increment the new resid
>>> NS> 16 incr start
>>> NS> 17 }
>>> NS> 18 $sel delete
>>> NS> 19 return
>>> NS> 20}
>>> NS> #======================================
>>> NS> However, the proc doesn't work with a simple system of 214 identical
>>> NS> residues (it's a membrane bilayer). When I use the 'residue' keyword
>>> at NS> line 7, I obtain a list of 218 'residue' which is wrong. But when I
>>> do NS> the same thing using the 'resid' keyworkd, I obtain a correct list
>>> of NS> 214 'resid'. Why do the 'residue' keyword give me 4 more residues?
>>> (When NS> I do the renumbering, the resids start to be wrong at 200)
>>>
>>> please check, whether those resids have been actually overwritten.
>>> see above.
>>>
>>> cheers,
>>> axel.
>>>
>>> NS>
>>> NS> Thanks for your help. I hope I'm not too confusing with all this
>>> NS> 'residue' and 'resid'
>>> NS>
>>> NS>
>>> NS>
>>> NS> Nicolas
>>> NS>
>>> NS>
>>>
>>>
>>>
>
>
>
>