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Questions and answers => MD simulations => Topic started by: dailiang on January 21, 2016, 07:55:22 pm

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Title: generate DNA pdb file for Gromacs
Post by: dailiang on January 21, 2016, 07:55:22 pm
The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

The reason why I ask this question is because I am using X3DNA to generate initial DNA conformation for MD simulations by Gromacs.

In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.
Title: Re: generate DNA pdb file for Gromacs
Post by: xiangjun on January 21, 2016, 10:07:55 pm
Hi,

Quote
The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

3DNA fiber or rebuild-generated DNA structures in PDB do not have special designation of terminal bases, such as A3, A5 etc. In my understanding, these names are non-standard. Overall, 3DNA-generated DNA structures follow the PDB format.

I am not a practitioner of molecular dynamics (MD) simulations. From reading, however, I believe even DNA structures downloaded directly from RCSB PDB (such as the Dickerson dodecamer 355d (http://www.rcsb.org/pdb/explore/explore.do?structureId=355d)) is not suitable for MD studies. Some preparation steps must be taken (including attaching hydrogen atoms, adding positive charges to neutralize the system, etc., in addition to distinguishing the four terminal nucleotides) before being fed into a MD software package. I am not sure if the different MD packages (AMBER, CHARMM, and Gromacs) follow the same input format, regarding terminal bases, among other details. Most likely, each MD package will be (slightly) different even in input format. Any comments?

In short, 3DNA does not aim to fit into any particular MD format for DNA structures in PDB. Users need to perform package-specific customizations of 3DNA-generated PDB structures, just as those downloaded from RCSB PDB.

Quote
In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.

To get  (DA, DT, DC, DG) instead of (A, T, C, G), please specify the -pdbv3 option to 3DNA fiber or rebuild. For example, the following command generate a B-DNA duplex with sequence AAAACCCTTT:

Code: [Select]
fiber -pdbv3 -seq=AAAACCCTTT 3dna-BDNA.pdb
And the PDB file looks like below:

Code: [Select]
REMARK    3DNA v2.3-2016jan20, created and maintained by Xiang-Jun Lu (PhD)
ATOM      1  P    DA A   1      -0.356   9.218   1.848  1.00  1.00           P
ATOM      2  OP1  DA A   1      -0.311  10.489   2.605  1.00  1.00           O
ATOM      3  OP2  DA A   1      -1.334   9.156   0.740  1.00  1.00           O
ATOM      4  O5'  DA A   1       1.105   8.869   1.295  1.00  1.00           O
ATOM      5  C5'  DA A   1       2.021   8.156   2.146  1.00  1.00           C
ATOM      6  C4'  DA A   1       2.726   7.072   1.355  1.00  1.00           C
ATOM      7  O4'  DA A   1       1.986   5.817   1.352  1.00  1.00           O
ATOM      8  C3'  DA A   1       2.952   7.370  -0.127  1.00  1.00           C
ATOM      9  O3'  DA A   1       4.210   6.832  -0.518  1.00  1.00           O
ATOM     10  C2'  DA A   1       1.848   6.598  -0.850  1.00  1.00           C
ATOM     11  C1'  DA A   1       1.913   5.344   0.016  1.00  1.00           C
ATOM     12  N9   DA A   1       0.711   4.472  -0.101  1.00  1.00           N
ATOM     13  C8   DA A   1      -0.589   4.841  -0.292  1.00  1.00           C
ATOM     14  N7   DA A   1      -1.415   3.843  -0.354  1.00  1.00           N
ATOM     15  C5   DA A   1      -0.604   2.728  -0.192  1.00  1.00           C
ATOM     16  C6   DA A   1      -0.881   1.351  -0.162  1.00  1.00           C
ATOM     17  N6   DA A   1      -2.113   0.841  -0.301  1.00  1.00           N
ATOM     18  N1   DA A   1       0.158   0.514   0.016  1.00  1.00           N
ATOM     19  C2   DA A   1       1.380   1.027   0.154  1.00  1.00           C
ATOM     20  N3   DA A   1       1.758   2.286   0.143  1.00  1.00           N
ATOM     21  C4   DA A   1       0.700   3.103  -0.037  1.00  1.00           C
ATOM     22  P    DA A   2       5.130   7.667  -1.527  1.00  1.00           P
ATOM     23  OP1  DA A   2       5.914   8.669  -0.770  1.00  1.00           O
ATOM     24  OP2  DA A   2       4.303   8.192  -2.635  1.00  1.00           O
ATOM     25  O5'  DA A   2       6.107   6.526  -2.080  1.00  1.00           O
ATOM     26  C5'  DA A   2       6.430   5.410  -1.229  1.00  1.00           C
ATOM     27  C4'  DA A   2       6.362   4.119  -2.020  1.00  1.00           C
ATOM     28  O4'  DA A   2       5.026   3.539  -2.023  1.00  1.00           O
....
HTH,

Xiang-Jun
Title: Re: generate DNA pdb file for Gromacs
Post by: dnalectronics on October 27, 2021, 01:00:46 pm
Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University