Dear Brittany,
Did you use R.E.D. Server Dev./PyRED ?
at
http://q4md-forcefieldtools.org/REDServer-Development/
See
http://q4md-forcefieldtools.org/REDServer-Development/images/PyRED.gif
You need to know:
- the total charge of the fragment to be connected?
use the MOLECULE1-INTRA-MCC1 keyword
- if the open valency is a head or tail
use the MOLECULE1-MOL3HEAD keyword
see the mol3 file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
PyRED generates FF lib. with atom types for molecular fragments + FF
parameter files + a LEaP script.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
Your linker is connected to the 5' terminal end; i.e. let's do:
xleap -f leaprc.ff99SB
> charge DC5
Total unperturbed charge: -0.307900
Total perturbed charge: -0.307900
> charge DT5
Total unperturbed charge: -0.307900
Total perturbed charge: -0.307900
-> it looks like this is the target value you need to match.
> desc DC5
UNIT name: DC5
Head atom: null
Tail atom: .R<DC5 1>.A<O3' 28>
Contents: R<DC5 1>
-> it looks like you need to generate a tail; not a head.
about your linker:
it looks like your linker is a polymer; here pay attention to the
conformation of that polymer; a way limit the conformation variability
of this polymer is to build it from its elementary building block;
i.e. CH3-OCH2CH2-OH
CH3-OCH2CH2-OH -> (1) OCH2CH2
(2) CH3-OCH2CH2
(3) OCH2CH2-OH
PEG = (2)-(1)n-(3)
See examples in REDDB:
http://q4md-forcefieldtools.org/REDDB/projects/F-84/
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
regards, Francois
> I am working on trying to attach a organic linker to two single
> stranded DNA at separate ends to mimic the experimental ring-like
> structure of the proximity effect. The linker is attached to the
> DNA through a phosphate group at the 5' and 3' ends. The organic
> linker has two capped phosphate groups. I compared my system to the
> AMBER tutorial A1. I developed RESP charges for the linker.
> Developing the parameters for the linker was a bit of a hassle.
> Then I proceeded to run the linker through LEAP. This was
> successful after I established unique atom types, but this was done
> through copying and pasting from a .mol2 file to the linker pdb file
> to run in LEAP. How do you develop unique atom types for the
> molecule using AMBER if it does not already do it? I was successful
> in running the DNA (polyAT decamer) in LEAP. LEAP did create a
> H5T atom but that could easily be removed by a visualizer method.
> I deleted one side of the DNA (polyAT to ployA). Before I
> proceeded to put them together, I deleted the phosphate capped ends
> from the linker and added a phosphate group to the 5' end of the
> DNA. I used Chimera combine command to link the structure. Using
> Join models, I highlighted the two ends I wanted attached and
> linked them together, unfortunately this software did not allow me
> to construct the whole complex. When I tried to run half of the
> created structure ,the biggest problem I feel is AMBER did not see
> the fixed group (phosphate group) that puts two individual
> structures together.
>
>
>> From all this being said, is there a way to attach DNA to a organic
>> linker, have readable atom types, notice the attached groups,
>> develop parameters, and run the whole structure though LEAP to
>> start simulations?
>
>
> I know I am not the first to want to attach DNA to a linker at two
> separate ends. I know there is someone who can guide me in the right
> direction.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 02 2014 - 23:30:02 PST
