Re: [gmx-users] Hbonds between Adenine and Thymine

2012-12-02 Thread Justin Lemkul
7 17DTH2'2 1357 8.908 9.903 3.047 1.7584 -0.8510 1.3980 17DT O3' 1358 8.813 10.100 3.193 -0.3350 0.2178 0.0665 Thanks in advance, Best regards, Hovakim От: Justin Lemkul Кому: Hovakim Grabski ; Discussion list for GROMA

RE: [gmx-users] Hbonds between Adenine and Thymine

2012-12-02 Thread Hovakim Grabski
.2313 -0.2753 -0.2747    17DT    H2'2 1357   8.908   9.903   3.047  1.7584 -0.8510  1.3980    17DT     O3' 1358   8.813  10.100   3.193 -0.3350  0.2178  0.0665 Thanks in advance, Best regards, Hovakim От: Justin Lemkul Кому: Hovakim Grabski ; Discuss

Re: Отв: [gmx-users] Hbonds between Adenine and Thymine

2012-11-29 Thread Justin Lemkul
On 11/29/12 2:04 PM, Hovakim Grabski wrote: Dear Justin, I only used pdb2gmx when I prepared the DNA which I created with nab. and the command that I used was: make_ndx -f md_0_1.gro -o index.ndx after that then I press r10 and r17 I get : 14 r_10:64 atoms 15 r_17

Re: [gmx-users] Hbonds between Adenine and Thymine

2012-11-29 Thread Justin Lemkul
ce, Best regards, Hovakim *От:* Justin Lemkul *Кому:* Hovakim Grabski ; Discussion list for GROMACS users *Отправлено:* четверг, 29 ноября 2012 1:33 *Тема:* Re: [gmx-users] Hbonds between Adenine and Thymine On 11/28/12 3:43 PM, Hovakim Grabski wrote: > De

Re: [gmx-users] Hbonds between Adenine and Thymine

2012-11-29 Thread Erik Marklund
Hi, A general note: make_ndx and index files are not magical in any way. You can usually construct an index group from e.g. a pdb file with awk. It's just lists of atom indices. Best, Erik 28 nov 2012 kl. 22.33 skrev Justin Lemkul: > > > On 11/28/12 3:43 PM, Hovakim Grabski wrote: >> Dear

Re: [gmx-users] Hbonds between Adenine and Thymine

2012-11-28 Thread Justin Lemkul
On 11/28/12 3:43 PM, Hovakim Grabski wrote: Dear Gromacs users, I set a simulation of 26 base pairs of DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine bu

[gmx-users] Hbonds between Adenine and Thymine

2012-11-28 Thread Hovakim Grabski
Dear Gromacs users, I set a  simulation of 26 base pairs  of  DNA with Ethidium Bromide for 5 ns. After a while Thymine rotated for about 70 degrees and then returned to its initial position. I wanted to find out hbonds between Adenine and Thymine but with make_ndx things don't work so well. How