[gmx-users] hdb file

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 1 23:25:35 CEST 2010

Moeed wrote:
> Dear Justin,
> Thanks so much for your help. The structure looks almost fine now.
> 1-I am getting bond distance of 1.52 or 1.53 and angles of 112.2 / 112.0 
> with -d 0.0584/ 0.0581. Actually when I open up the same structure file 
> in VMD at different times I see even a little difference in bond 
> distance between atoms *on* the 4C unit chain (1.54 , 1.53 A). Thats why 
> I though maybe 1 or 2 degrees difference from equilibrium value of 110 
> for connecting atoms does not influence results..But still I wanted to 
> make sure if I need to do energy minimization to get exact value of 110 
> for angles between repeating units and if this is going to affect 
> simulation results?

You should probably always do EM.

> 2- I am trying to obtain top and gro file including H atoms with hdb abd 
> rtp files. I am not getting any error messages and it seems everything 
> is going well but the gro file after adding H s has a very weird 
> structure. I doubt I have wriiten hdb file correctly. Could you please 
> take a look at it?

You're right - your .hdb file is not correct.

The control atoms define the geometry about the atom to which H atoms are added. 
  If you're always using the next (+C1) or previous (-C4) atoms of another 
residue, that won't be right.  Study the logic of my original .hdb file to get 
the pattern.  Basically it was always the C atom "before" and "after" the target 
carbon in the chain, so only C1 and C4 of each internal residue should ever make 
reference to other residues.  I think that should work but I haven't tried it, 
nor do I have time to.


> *with hdb file*
> Eth     4
> 2       6       H1      C1      C2      -C4
> 2       6       H2      C2      C1      +C1
> 2       6       H3      C3      C2      +C1
> 2       6       H4      C4      C3      +C1
> EthB    4
> 3       4       H1      C1      C2      +C1
> 2       6       H2      C2      C1      +C1
> 2       6       H3      C3      C2      +C1
> 2       6       H4      C4      C3      +C1
> EthE    4
> 2       6       H1      C1      C2      -C4
> 2       6       H2      C2      C1      -C4
> 2       6       H3      C3      C2      -C4
> 3       4       H4      C4      C3      -C4


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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