Messages

1

MD simulations / Re: errors when I run find_pair

« on: February 06, 2014, 03:46:01 pm »

Thanks for your careful checking!
This is a type of 5' terminal patch in CHARMM force field.
Beibei

2

MD simulations / Re: errors when I run find_pair

« on: February 06, 2014, 02:23:15 pm »

I am attaching my input pdb file and the results I got.

3

MD simulations / Re: errors when I run find_pair

« on: February 06, 2014, 02:06:46 pm »

Thank you! I figured out that.
But I still have another problem.
It says: more than one  O5' atoms : residue name 'CYT', chain A, number    *****the first atom is used*****
But in my pdb file, i just have one O5' atom. I use 5PHO patch for the 5' terminal, is the O5T atom identified as another O5' atom.
Beibei

4

MD simulations / errors when I run find_pair

« on: February 06, 2014, 01:44:23 pm »

Hello,
I want to do some analysis with x3dna-v2.1. At first I met the problem: open_file </home/user/x3dna-v2.1/BASEPARS/misc_3dna.par> failed: No such file or directory, and I changed the directory name from config to BASEPARS. But another error came: error reading upper HB criteria/alternative indicator. I do not know how to solve it. Can anyone help me?
Beibei