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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