Dear N Nandi,
> Thanks for your reply. To load the whole tRNA molecule including the
> 5'terminal phosphate group we tried to generate the parameter file
> for phosphate group using the HF method in antechamber. Following
> command was used:
> ./antechamber -i X.out -fi gout -o X.mol2 -fo mol2 -c resp
> but it showed that error in open QOUT file.
So if I understand you you want a 5'terminal phosphate group, while a
5'OH terminal group is present in the Amber force field topology
database.
The trick is that RNA central fragments have a total charge = -1
& the sum of a 5'-term fragment + the complementary 3'-term fragment
has a total charge = -1
> charge RA
Total unperturbed charge: -1.000000
> charge RA3
Total unperturbed charge: -0.691900
> charge RA5
Total unperturbed charge: -0.308100
this means you have to find a small molecule such as (-2)O3PO-Me or
(-2)O3PO-R that will lead to the '(2-)O3P-O' fragment and the later
fragment has to replace the 5'OH chemical group of the RA5 fragment
from the Amber force field topology database (or RC5 or RU5 etc...).
I would use R.E.D. or R.E.D. Server to do that; this is quite
straightforward when using the INTRA-MCC keyword... Then, you can
easily create RX5 manually (RA5 to whom the 5'OH group is removed)...
See the archives in the q4md-fft mailing list; recently we discussed
about a similar problem:
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft
regards, Francois
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Received on Fri Apr 12 2013 - 07:30:02 PDT
