Messages

1

RNA structures (DSSR) / Further questions about inter-base angle calculations

« on: February 27, 2017, 01:51:20 am »

In the last question, I want to calculate the inter-base angle of the TS state  of  an addition reaction occurred in a dinucleotide monophosphate.  While it was addressed for the TS state, the inter-base angle can not be obtained for the corresponding product even using the --nt-cutoff=0.9 option.  I want to know how can I calculate the inter-base angle of the product. Thanks very much! The pdb file is given in the attachment.


p.s.  According to my own test calculations, the reasons may be due to the  inter-base angle of the product exceeds the threshhold.

2

RNA structures (DSSR) / Re: Questions of calculations of inter-base angles

« on: February 25, 2017, 01:35:45 am »

Not MD simulations, the nearly vertical state (related picture is given in the attachment) corresponds to the TS state of the addition reaction between G/C8 and T/C5.

The question is addressed, Thanks very much! 

3

RNA structures (DSSR) / Questions of calculations of inter-base angles

« on: February 24, 2017, 11:56:58 pm »

Recently, I am trying to use X3DNA to calculate tentatively the inter-base angles in dinucleotide monophosphates. When the two bases are in the nearly canonical state, using the --non-pair option can put out the value of the inter-base angle. However, when the two bases are in a nearly vertical state, using the --non-pair option gives results like these:

Command: x3dna-dssr -i=1.pdb --non-pair -o=1.out
Date and time: Sat Feb 25 12:38:29 2017
File name: 1.pdb
    no. of DNA/RNA chains: 1 [A=1]
    no. of nucleotides:    1
    no. of atoms:          39
    no. of waters:         0
    no. of metals:         0

However, in the 1.pdb (please see the attachment), there are two nucleotides not one! In this case (1.pdb), I want to know whether or not X3DNA can give the value of the inter-base angle. If it can,  how to  set up the command lines? Thanks very much!