Hi,
I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond, Mn-O bond,... formed. Now i want to do MD simulation for this functionalized nanotube. (I use AMBER99SB ff)
How should i define ffbonded.itp?I have bond length and angles but i don't know kb(binding constant) If for example kb of Mn-O for another similar structures exists in literatures can i use them?
If kb doesn't exist, can i freeze this BOND(not the whole AA) on known bond length, ANGLE on known dihedral angle and known partial charges charges(all achieved after functionalization of NT with AA by DFT) or maybe constraint it?
Is it possible to freeze bond at all?! Is there any better choice?
Best regards
As you are using gromacs, LINCS usually constrains all bonds anyway. Having said that, it's not different from not having a reasonable kb at all, imho.
Thank you so much Norman Geist .Yes, i use GROMACS.
But GROMACS doesn't recognize for example Mn-O bond. so i need to define it in ffbonded.itp . you mean if i constraint all bonds it doesn't need to have their kb?? and i would not encounter any error related to?
You would still have to define the bond of course, but you don't need a kb necessarily. Depending on how you build your structure, it might be more reasonable to define the bond or constraint directly in your molcules itp file, instead of changing the ffbonded.itp.
Or, adding those residues to the definitions underlying pdb2gmx as e.g. specbonds.dat so the bonds are added automatically added based on distance.
Yeah. I've got it now.
Thank you Norman Geist for your kindly responses as always.
Best
Roja
If your Mn-CdS structure is not stable, you need to carefully revisit your parameterization. Fixing random Kbs to keep it rigid is fine, if you don't care about rigorous description of that region, but bear in mind you cannot say a lot about that part of your system. You might want to revisit some rigorous procedures for parameterizing such systems:
Article Force Field Parametrization of Colloidal CdSe Nanocrystals U...
Article A transferable force field for CdS-CdSe-PbS-PbSe solid systems
etc.
Of course you can add restraints or constraints to the bond length. However, this may trigger technical problem when you do some advance simulations.
For force field parameters derivation, the parameters should be obtained with frequency calculation under harmonic approximation. I think Ambertools and Gaussian would satisfy your needs.
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