VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Tue Nov 29 2005 - 03:22:52 CST

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>
-------------------------------