Moeed wrote:
Hello Justin,
Thanks for your help. Actually, I meant if I use -d option rather than
-box I would have better control on bond distance between monomer units.
By try and error I found out if I used -d 0.0017 the distance between
two adjacent C (2 monomer ends) is 1.54A. which is the bond length for
C-C in the molecule.
editconf -f prodrg.pdb -o prodrgD.gro -d 0.017 -bt cubic
There should be no trial and error here. It is a simple matter of geometry. As
long as you've found something that works...
1- To get CH2CH2CH2CH2 repeating unit I removed the H s from both ends
by deleting one of the H at each end of CH3CH2CH2CH3. My chemistry
background is not good, so I wanted to know if the difference in C-H
angle and CH2 as a result of removing the third H in CH3 is negligible.
Also the angle between C atoms at chain ends are not the same as those
within the chain. I have just manupulated the -d option so |
|
H
that bond distance is similar to that of C-C on backbone.
All the carbons have sp3 geometry, so I don't see the issue here.
I am guessing the answer is by using pdb2gmx the structure file will be
modified so that the mentioned angles are set properly. Please let me
know if I am right and this issue is remediable... How can I make sure
this is not going to affect the simulation given that I am going to
build up a very long chain..
If you remove hydrogens and let pdb2gmx build them for you with an appropriate
.hdb entry, the structure will be fine. You'll save yourself a lot of time by
actually doing things instead of waiting for me to tell you what to do. If you
encounter a problem, post a question. Otherwise, the best way to learn is by doing.
-Justin
Thanks for your attention.
moeed
--
========================================
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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