Messages

1

General discussions (Q&As) / Re: building a ssDNA

« on: April 18, 2011, 11:32:46 am »

It was just a requirement of the project I am doing. I wanted the ends of DNA to be different from the body. But this problem is solved. I manually changed the residues at both ends, in pdb file.

Thanks,
Majid

2

General discussions (Q&As) / Re: building a ssDNA

« on: April 09, 2011, 09:05:13 pm »

Hi Xiangjun,

I am creating .pdb file for a single strand dna by following the method you suggested. But this dna doesn't have asymmetric ends, while I need to cap it with 5' and 3'. Can you guide me how do make the ends 5', and 3'?

Thanks,
Majid

3

General discussions (Q&As) / Re: building a ssDNA

« on: April 09, 2011, 01:14:13 pm »

Yes, I suspect so too.

Thanks for your help,
Majid

4

General discussions (Q&As) / Re: building a ssDNA

« on: April 08, 2011, 02:37:35 pm »

Hi Xiangjun,

With 3DNA v2.0 I could create the single strand dna. But when I try to create the toplogy file (.top), it gives me following error: Fatal error:
Could only find a forcefield type for 119 out of 287 atoms

I am using the oplsaa forcefield, and I suspect it is because  atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached below. Could you guide me how to add all these possible bonds in my .n2t file?

Thanks,
Majid


atomname2type.n2t file

C    opls_157    -0.18   12.011   4    H 0.108   H 0.108   H 0.108   C 0.150
C    opls_158    -0.12  12.011   4    H 0.108   H 0.108   C 0.150   C 0.150
C    opls_157    0.145  12.011   4    H 0.108   O 0.141   H 0.108   C 0.150
C    opls_157    0.145  12.011   4    H 0.108   H 0.108   O 0.108   C 0.150
C    opls_158    0.205  12.011   4    H 0.108   C 0.150   O 0.140   C 0.150
C    opls_158    -0.06  12.011   4    H 0.108   C 0.150   C 0.150   C 0.150  
C    opls_145    -0.12  12.011   3    C 0.150   C 0.150   H 0.108
C    opls_145    -0.12  12.011    3    C 0.133   C 0.150   O 0.140
C    opls_235    0.5    12.011    3    C 0.133   N 0.140   O 0.140
C    opls_235    0.5    12.011    3    C 0.133   N 0.132   C 0.150
C    opls_235    0.5    12.011    3    C 0.133   N 0.132   H 0.108
O    opls_236    -0.5   15.9994 1    C 0.123
N    opls_238    -0.5   14.0067 3    H 0.108   C 0.140   C 0.150
N    opls_238    -0.5   14.0067 3    H 0.108   C 0.132   N 0.123
N    opls_238    0      14.0067 2    C 0.140   N 0.123
H    opls_140    0.06    1.008    1    C 0.108
H    opls_155    0.418   1.008   1    O 0.095
H    opls_241    0.30    1.008   1    N 0.095
O    opls_154    -0.683 15.9994 2    C 0.140   H 0.095
P    opls_393    1     30.97376 4    O 0.180   O 0.180   O 0.180   O 0.180
O    opls_395    -1     15.9994   2    P 0.180   H 0.095
O    opls_394    -1     15.9994 1    P 0.180
N    opls_237    0      14.0067 4    C 0.140   C 0.140   C 0.140   C 0.140
C    opls_240    0      12.011  3    C 0.142   C 0.142   C 0.142
C    opls_239    0      12.011  2    C 0.142   C 0.142

5

General discussions (Q&As) / Re: building a ssDNA

« on: April 08, 2011, 01:27:35 pm »

Okay, thanks Xiangjun! I have an older version of 3DNA, but I am going to upgrade it to  2.0.

Majid

6

General discussions (Q&As) / Re: building a ssDNA

« on: March 17, 2011, 06:48:42 pm »

Ok, this problem is solved. I set my environment variables but didn't change directory to X3DNA. When I issued the commands in that directory, it worked. But I have one more question. I am unable to find pdb_frag command in X3DNA/bin directory. I search it in X3DNA as well but couldn't find it. And its not mentioned in 3DNA manual as well. Do I have to get it separately?

Thanks,
Majid

7

General discussions (Q&As) / Re: building a ssDNA

« on: March 17, 2011, 06:17:38 pm »

Hi Xiangjun,

I tried out the procedure you mentioned to create ssDNA.pdb. But in the last step (after entering number of steps = 1), I get following error "Number of repeats (Dft: 10): 1
open_file <my_seq.pdb> failed: Permission denied
". I used to get such errors in gromacs when it wasn't installed in my home folder, and I needed root permission to write. But, 3DNA is located in my home folder, so I am not sure why am I getting this. Could you help me with this?

Thanks,
Majid

8

General discussions (Q&As) / Re: building a ssDNA

« on: March 08, 2011, 07:00:18 pm »

Okay, thanks Xiangjun! I'll try that.

9

General discussions (Q&As) / building a ssDNA

« on: March 07, 2011, 10:29:41 pm »

Dear All,

I just started using 3DNA. I want to build a pdb file for single strand DNA that I can use in gromacs to simulate interaction between DNA and CNT. I skimmed through the manual, but don't understand how to get started. Could anyone please highlight what should I look into to create this pdb file?

Thanks,
Majid