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Questions and answers > MD simulations
generate DNA pdb file for Gromacs
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dailiang:
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.
xiangjun:
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?
--- End quote ---
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) 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.
--- End quote ---
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: ---fiber -pdbv3 -seq=AAAACCCTTT 3dna-BDNA.pdb
--- End code ---
And the PDB file looks like below:
--- Code: ---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
....
--- End code ---
HTH,
Xiang-Jun
dnalectronics:
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.
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.