[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.
-Justin
> *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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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