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 !