VMD-L Mailing List

From: Streutker, J (j.streutker_at_st.hanze.nl)
Date: Thu Dec 07 2006 - 04:40:24 CST

Hi everyone,
 
I`m having trouble with VMD. I`m using trajectory and PDB file, so simulate a lipid bilayer. All of this is done coarse-grained, so I only have partial amino acids (# atoms ranges from 1 to 3), instead of complete amino acids. A part of my trajectory contains 5 helices, but I cant get VMD/stride te draw them as (new)ribbons (or some other kind of helix shape). If I`m not mistaken, ribbons are drawn through the CA atoms of each aminoacid. And my file contains all CA atoms, from every molecule from the helix. But nothing seems to appear. When I select Tubes, I get an error: Internal error in draw_tube for CA atoms: last_resid = 2 but no first atom was added. So I thought: I cheat and rename every molecule to CA. Unfortunately that didnt work either. Well it works partially. I get some lines and bends, but no real helix shape. After this I didnt really know what to do next, so I used PSFgen to complete the aminoacids. This worked, I see helices. There is only one major problem: some H atoms and every O and C at
om at the end of a aminoacid, get the coordinates: 0.0, 0.0, 0.0. Adding to that, they also have an atomic charge of -1.0 in the psf file. So it is happing every time, with the same kind of atom, but why? perhaps it has something to do with the fact that the are added by PSFgen, although most of the are placed correctly by PSFgen...
 
 
Kind regards,
 
J. Streutker
University of Groningen
Netherlands