VMD-L Mailing List

From: Luis Rosales (ludwig_at_biomedicas.unam.mx)
Date: Tue Apr 05 2005 - 02:47:11 CDT

 
Hi Luis,

Como estás??

The records are ATOM records, the structure is the 1JJZ entry from the PDB,
I could send it to you if you want to take a closer look at the file:

ATOM 1 N ASN A 8 -6.450 1.378 3.923 1.00 0.00
N
ATOM 2 CA ASN A 8 -6.782 1.512 5.331 1.00 0.00
C
ATOM 3 C ASN A 8 -6.609 0.159 6.024 1.00 0.00
C
ATOM 4 O ASN A 8 -7.177 -0.075 7.090 1.00 0.00
O
ATOM 5 CB ASN A 8 -8.236 1.954 5.514 1.00 0.00
C
ATOM 6 CG ASN A 8 -8.404 3.438 5.182 1.00 0.00
C
ATOM 7 OD1 ASN A 8 -7.608 4.281 5.563 1.00 0.00
O
ATOM 8 ND2 ASN A 8 -9.483 3.710 4.454 1.00 0.00
N
ATOM 9 H ASN A 8 -5.709 1.971 3.606 1.00 0.00
H
ATOM 10 HA ASN A 8 -6.099 2.269 5.716 1.00 0.00
H
ATOM 11 1HB ASN A 8 -8.885 1.358 4.873 1.00 0.00
H
ATOM 12 2HB ASN A 8 -8.549 1.770 6.543 1.00 0.00
H
ATOM 13 1HD2 ASN A 8 -10.097 2.972 4.174 1.00 0.00
H
ATOM 14 2HD2 ASN A 8 -9.680 4.652 4.185 1.00 0.00
H
ATOM 15 N GLY A 9 -5.822 -0.696 5.389 1.00 0.00
N
etc...

I was thinking that maybe generating a PSF file for the peptide could help,
but I havent found the right way to patch the first and the last residue to
keep the bond between them, as this is a cyclic peptide...

Thanks, Luis

> -----Original Message-----
> From: Luis Gracia [mailto:lug2002_at_med.cornell.edu]
> Sent: Monday, April 04, 2005 10:08 PM
> To: Luis Rosales
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: VMD and Cyclotides...
>
> Are the atom in the pdb file HETATM or ATOM?
> Luis
>
> Luis Rosales said the following on 04/04/05 21:05:
>
> >Hi,
> >
> >I am trying to visualize a cyclic peptide (cyclotide),
> however I found that
> >VMD does not recognize it as a protein. So I am unable to
> see the ribbons and
> >the trace representations. I checked the PDB file and it
> does look like a
> >normal PDB NMR-determined file...
> >
> >I believe that the problem could be on the extra C-term N-term bond.
> >Any ideas about how can this problem be solved??
> >
> >Thanks,
> >
> >Luis
> >
> >--
> >Open WebMail Project (http://openwebmail.org)
> >
> >
>