Print Page - generate DNA pdb file for Gromacs

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

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.6.0 (DSSR Manual) · Homepage

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.

Title: Re: generate DNA pdb file for Gromacs
Post by: ZMY on August 28, 2025, 07:05:11 am

Dear all,

We are currently attempting to model non-natural nucleic acid structures. We would like to know if it is possible to predict the structure of threose nucleic acid (TNA). Is this feature already included in some of the tools ?

The main difference between TNA and DNA or RNA lies in the ribose. It is known that DNA (RNA) contains a pentose sugar, while TNA contains a tetrose sugar. Therefore, the connection sites of the phosphodiester bonds are different.

Thank you in advance,
Best regards, Mengyao

Title: Re: generate DNA pdb file for Gromacs
Post by: xiangjun on September 13, 2025, 10:45:00 am

Quote

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.

With DSSR (here v2.6.0-2025jul24 is used), you can use the following command to generate a PDB file for your (DNA) sequence:

Code: Bash

x3dna-dssr fiber --seq= A6C10 --repeat =2 --model =RNA
x3dna-dssr fiber --rna -o=rna -ss.pdb
x3dna-dssr fiber --rna -ds -o=rna - duplex .pdb # --rna -double , --RNA - duplex
x3dna-dssr fiber --g4 -o=g4.pdb
 
# The following four commands lead to the same results
x3dna-dssr fiber --seq= A6TC9 --repeat =2 -o=B1.pdb
x3dna-dssr fiber --B-DNA --seq= A6TC9 --repeat =2 -o=B2.pdb
x3dna-dssr fiber --model =b-dna --seq= A6TC9 --repeat =2 -o=B3.pdb
x3dna-dssr fiber --model =b-dna --seq=A6 -T-C9 --repeat =2 -o=B4.pdb
 
x3dna-dssr fiber --seq= A1000 --mmcif - output # B-DNA , in mmCIF output format
 
x3dna-dssr fiber --pauling --seq=A6 # three strands , all A6
x3dna-dssr fiber --pauling --seq=C6: # one strand : C6 ( A )
x3dna-dssr fiber --pauling --seq=A6:G2 # two strands : A6 ( A ) and G2 ( B )
x3dna-dssr fiber --pauling --seq=A6 :: G2 # two strands : A6 ( A ) and G2 ( C )
x3dna-dssr fiber --pauling --seq =: U3:G2 # two strands : U3 ( B ) and G2 ( C )
x3dna-dssr fiber --pauling -dna --seq=U8 --repeat =4 # U converted to T

See the DSSR User Manual (http://docs.x3dna.org/dssr-manual.pdf), especially Section "5.2 Regular helical models (fiber)" for more details.

Title: Re: generate DNA pdb file for Gromacs
Post by: xiangjun on September 13, 2025, 11:04:50 am

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?

DSSR has superseded X3DNA, and it can be used to generate a PDB file with terminal bases as you requested. See the following example:

Code: [Select]

# Generate a regular B-DNA model with sequence (AAAAAATTTTTT; shortened as A6T6)
x3dna-dssr fiber --b-dna --seq=A6T6 -o=A6T6-BDNA.pdb

# Mutate residue name 5'-A on chains A and B from the detault 'A' to 'A5':
x3dna-dssr mutate --entry='num=1 to=A5' -i=A6T6-BDNA.pdb -o=A5-both.pdb

A portion of the output PDB file A5-both.pdb is shown below:

REMARK PDB mutated using DSSR
REMARK DSSR mutate: A.A1 to A5
ATOM      1  P    A5 A   1      -0.356   9.218   1.848  1.00  0.00           P
ATOM      2  OP1  A5 A   1      -0.311  10.489   2.605  1.00  0.00           O
ATOM      3  OP2  A5 A   1      -1.334   9.156   0.740  1.00  0.00           O
ATOM      4  O5'  A5 A   1       1.105   8.869   1.295  1.00  0.00           O
ATOM      5  C5'  A5 A   1       2.021   8.156   2.146  1.00  0.00           C
ATOM      6  C4'  A5 A   1       2.726   7.072   1.355  1.00  0.00           C
ATOM      7  O4'  A5 A   1       1.986   5.817   1.352  1.00  0.00           O
ATOM      8  C3'  A5 A   1       2.952   7.370  -0.127  1.00  0.00           C
ATOM      9  O3'  A5 A   1       4.210   6.832  -0.518  1.00  0.00           O
ATOM     10  C2'  A5 A   1       1.848   6.598  -0.850  1.00  0.00           C
ATOM     11  C1'  A5 A   1       1.913   5.344   0.016  1.00  0.00           C
ATOM     12  N9   A5 A   1       0.717   4.478  -0.101  1.00  0.00           N
ATOM     13  C8   A5 A   1      -0.592   4.850  -0.293  1.00  0.00           C
ATOM     14  N7   A5 A   1      -1.424   3.839  -0.355  1.00  0.00           N
ATOM     15  C5   A5 A   1      -0.609   2.726  -0.193  1.00  0.00           C
ATOM     16  C6   A5 A   1      -0.886   1.349  -0.163  1.00  0.00           C
ATOM     17  N6   A5 A   1      -2.111   0.835  -0.301  1.00  0.00           N
ATOM     18  N1   A5 A   1       0.154   0.505   0.016  1.00  0.00           N
ATOM     19  C2   A5 A   1       1.380   1.020   0.154  1.00  0.00           C
ATOM     20  N3   A5 A   1       1.767   2.294   0.144  1.00  0.00           N
ATOM     21  C4   A5 A   1       0.712   3.105  -0.035  1.00  0.00           C
ATOM     22  P     A A   2       5.130   7.667  -1.527  1.00  0.00           P
ATOM     23  OP1   A A   2       5.914   8.669  -0.770  1.00  0.00           O
ATOM     24  OP2   A A   2       4.303   8.192  -2.635  1.00  0.00           O

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.

I'm not sure the exact requirements for compatibility with Gromacs, but you can easily mutate 'A' to 'DA' etc using DSSR mutate subcommand as shown below:

Code: [Select]

x3dna-dssr mutate --entry='A:DA;T:DT' -i=A6T6-BDNA.pdb -o=DA-DT.pdb
See the DSSR User manual (http://docs.x3dna.org/dssr-manual.pdf) for more details.

Title: Re: generate DNA pdb file for Gromacs
Post by: xiangjun on September 13, 2025, 11:13:30 am

Hi Mengyao,

Thanks for posting your question on the 3DNA Forum.

Quote

We are currently attempting to model non-natural nucleic acid structures. We would like to know if it is possible to predict the structure of threose nucleic acid (TNA). Is this feature already included in some of the tools ?

The main difference between TNA and DNA or RNA lies in the ribose. It is known that DNA (RNA) contains a pentose sugar, while TNA contains a tetrose sugar. Therefore, the connection sites of the phosphodiester bonds are different.

I am not familiar with TNA. From your description, TNA is a non-natural nucleic acid structure with a tetrose, instead of pentose, sugar. Given further information about TNA, I may be able to help build a model as a starting structure for MD simulations.

Best regards,

Xiang-Jun

Title: Re: generate DNA pdb file for Gromacs
Post by: rkumar on September 29, 2025, 07:45:22 am

Hi,

Another option could be the Nucleic Acid Builder (NAB) (available in AmberTools) to model the 3D structure of DNA for MD simulations (https://ambermd.org/tutorials/basic/tutorial1/section2.php). I have used this one to model the DNA and performed the MD simulations.

Thanks,
Rajendra

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