VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Mon Dec 05 2005 - 03:24:16 CST

Hi John,
thanks for your kind answer. As a debugger, I can try it the new vmd-build.
Thanks

andrea

John Stone wrote:

>Andrea,
> I've got a new VMD build that merges in CONECT records with the
>automatic distance-based bond search now. The new code will also let
>you disable either of the PDB CONECT records or the automatic bond search
>so you can override this behavior if you want. Let me know if you want to
>try this new build, it's not posted on the web yet.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Tue, Nov 29, 2005 at 10:22:52AM +0100, andrea spitaleri wrote:
>
>
>>Hi all,
>>thanks for fixing this "issue". However, I have noticed another
>>"problem". I have got a file.pdb and it is visualised properly. After
>>feeding it to the gromcas tools (such as pdb2gmx or editconf ), the
>>terminus aminoacid seems unbonded. In fact, if I select "protein", the
>>terminus residue is not selected. That's strange since in gromacs
>>topology file the C-N bond is still there. The bond distance is within
>>the cutoff, I guess.
>>
>>
>>Regards,
>>
>>andrea
>>
>>John Stone wrote:
>>
>>
>>
>>>Hi,
>>>I think that doing what others suggested is the best thing in the short
>>>term, but I wanted to mention that I now have CONECT record reading in the
>>>VMD PDB reader, and I'm working on making it do the right thing since most
>>>PDB files only have CONECT records for a small subset of the bonds in the
>>>system (usually only the unusual ones). I've got a bit more work to do,
>>>but
>>>when it's done this will "just work", in the future.
>>>
>>>John
>>>
>>>On Tue, Nov 22, 2005 at 02:03:52PM +0100, andrea spitaleri wrote:
>>>
>>>
>>>
>>>
>>>>Hi all,
>>>>I have a file.pdb with CONECT flag at the end giving the S-S connection
>>>>atom numbers. While in pymol or insight I can see the S-S bond,
>>>>in vmd it doesn't appear at all. I am wondering if it is a problem of
>>>>cutoff since the dist is quite large (0.25nm).
>>>>Any help??
>>>>
>>>>Regards,
>>>>Andrea
>>>>--
>>>>-------------------------------
>>>>Andrea Spitaleri
>>>>Dulbecco Telethon Institute
>>>>c/o DIBIT Scientific Institute
>>>>Biomolecular NMR, 1B4
>>>>Via Olgettina 58
>>>>20132 Milano (Italy)
>>>>Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
>>>>-------------------------------
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>--
>>-------------------------------
>>Andrea Spitaleri
>>Dulbecco Telethon Institute
>>c/o DIBIT Scientific Institute
>>Biomolecular NMR, 1B4
>>Via Olgettina 58
>>20132 Milano (Italy)
>>Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
>>-------------------------------
>>
>>
>
>
> 

-- 
-------------------------------
Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
-------------------------------