Dear all: I read the paper "Performance of Empirical Potentials (AMBER, CFF95, CVFF, CHARMM,OPLS, POLTEV), Semiempirical Quantum Chemical Methods (AM1,MNDO/ M, PM3), and Ab Initio Hartree]Fock Method for Interaction of DNA Bases: Comparison with Nonempirical Beyond Hartree]Fock Results" publish on jcc 1996 I am intested in the H-bonded GC base pairs. and the author mentioned them in the supporting information. but I didn't find the right parameter for it withou the sidechain. if anybody knows, please tell me about it , thank you very much!
Dear sir: thank you for your reply. what I mean G/C pair is the guanine and the cytosine, and I want to do MD simulation about H-bonded G/C pairs. Now, I don't find the right topology for these. but there are tautomers in toppar/stream subdir. and they are not the one I need. is it possible that I just delete the sidechain and add H atom for Guanine and Cytosine ? and is it Ok if I care the H-bond much ? thank you for your help!
Dear sir, the simulation is going well now, thanks very much ! but here comes another problem : the G/C base were initially placed in a plane , but after a serial of minimization in the water box, they become perpendicular. is it normal ? how can this happen ? is it something to do with the vdW parameter or something else ? thank you very much !
Although H-bonds stabilize the double helix, H-bonds alone may not make the G-C and A-T pairs stable individually, w/o the DNA scaffolding. The free bases in solution have too many other degrees of freedom available. Water will also form H-bonds with the polar parts of the bases.
roger that, thank you sir but what do you mean about "w/o the DNA scaffolding" ? is it some way to enforce them on a plane ? maybe I shall go on the equilibrium step, they might be on a plane after a long time and become stable. thank you very much !
I mean that the phosphodeoxyribose backbone and additional base pairs are needed to get stable H-bonds. Experimentally, most biological helices require a couple turns of the helix in order to be stable in aqueous solution.
I see others's work (year 1997) using CHARMM23 parameter doing MD of the GC pair are quite stable , after MD simulation, the two bases are in a plane, but in my case, during 1ns equilibrium step, the G-C pair flying apart though they are H-bonded in the first 250ps. is it something to do with the initial sturcture ? and is it any way to make them more stable in a plane ? thank you very much !
you are right, I shall take more respect of the results. in the paper mentioned above, they didn't mention the solvation box, they should just do it only with base pairs. but what shall I do with my simulation of G-C pair in water box, it seems all right that the bases fly apart or they form stacking but not pair during equilibrium step. but I can't perform vibrational analysis to check the H-bond effect on the sturcture. but is it still meaningful go on the simulation and check the sturctural fluctuation? and by the way, is there any already published paper about base pair simulation ? I didn't find about G-C pair yet. thank you for your time !