Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem...
Thanks,
Alex
>
Hi Alex,
I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA
ACGT
You would generate
TACGTA
Then
Hi Alex,
I think the best way is to extend the chain, such that you get an overlap
between both ends. So for a stretch of DNA
ACGT
You would generate
TACGTA
Then you strip off the terminal atoms and rewire the links over the
boundary. It requires renumbering the topology and at first looks a b
JL> The force field parameters for a phosphodiester are the same in a linear,
finite
JL> DNA as they will be in your infinite chain.
I didn't mean that anything would need to be changed in the description of
residues. The FF handles a
finite chain perfectly.
JL> The problem is in telling pdb2gm
On 4/25/15 11:34 PM, Alex wrote:
Justin,
I am not entirely sure I understand your sequence of steps. Why do you
want to first run it normally, but then also without adding the
hydrogens? The hydrogens (a total of two) are only added at the
termini by default, and in the final product there's n
Justin,
I am not entirely sure I understand your sequence of steps. Why do you
want to first run it normally, but then also without adding the
hydrogens? The hydrogens (a total of two) are only added at the
termini by default, and in the final product there's no
need for them anyway.
Here's what
Yeah, I was trying to avoid that last part. You can tell by now how much I
dislike uhm doing work. :) I'll try it, thanks.
Alex
JL> 4. Manually edit the topology to introduce the needed bond, angles, and
dihedrals.
JL> -Justin
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On 4/25/15 12:00 AM, Alex wrote:
Ahoy,
What I have here is a 100% precisely set up periodic ssdna chain of
six residues without termini. The goal is to get the 'polymerization'
across the box. So, I boxed the chain and set up the periodicity pretty much
perfectly.
To test, translation in the
Ahoy,
What I have here is a 100% precisely set up periodic ssdna chain of
six residues without termini. The goal is to get the 'polymerization'
across the box. So, I boxed the chain and set up the periodicity pretty much
perfectly.
To test, translation in the direction of periodicity by the
perio
