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bond parameters/SASA optimization for a new molecule
- fralav
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2 years 6 months ago #9199
by fralav
bond parameters/SASA optimization for a new molecule was created by fralav
Hi, I'm trying to parametrize a lipopeptide by following the tutorial about parametrization of a new small molecule.
I'm currently at the stage where I have optimized the bonded parameters of my molecule in order to match as much as possible the reference atomistic distributions.
Then I calculated the SASA for all the versions of my molecule's parameters and I have found that the best agreement of the CG SASA compared to the AA is reached for the non optimized topology, that is the one for which the distributions of bond lenghts and angles fit less with the AA distributions. In the first model, with bonded parameters not optimized, the % of discrepancy between CG and
AA SASa is 1.8%, wehereas in the case of the optimized parameters it become around 6.8%
I have to specify that my molecule contains some standard residues and some non natural aminoacids and initially I kept the parameters of the standard amino acidic residues fixed to the published values, but then I modified them also because the distributions of the CG bonded parameters were not fitting with the AA distributions, also for the standard residues.
I would like to understand I can I manage with this issue. Should I "trust" more the bonded parameters distributions or the SASA calculations? Unfortunately for my molecule there are not experimental partition data available and I can't compare that.
thank you for your help!
I'm currently at the stage where I have optimized the bonded parameters of my molecule in order to match as much as possible the reference atomistic distributions.
Then I calculated the SASA for all the versions of my molecule's parameters and I have found that the best agreement of the CG SASA compared to the AA is reached for the non optimized topology, that is the one for which the distributions of bond lenghts and angles fit less with the AA distributions. In the first model, with bonded parameters not optimized, the % of discrepancy between CG and
AA SASa is 1.8%, wehereas in the case of the optimized parameters it become around 6.8%
I have to specify that my molecule contains some standard residues and some non natural aminoacids and initially I kept the parameters of the standard amino acidic residues fixed to the published values, but then I modified them also because the distributions of the CG bonded parameters were not fitting with the AA distributions, also for the standard residues.
I would like to understand I can I manage with this issue. Should I "trust" more the bonded parameters distributions or the SASA calculations? Unfortunately for my molecule there are not experimental partition data available and I can't compare that.
thank you for your help!
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