[gmx-users] building up a polymer chain

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 23 19:27:01 CEST 2010

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.


> Thanks for your attention.
> moeed


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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