Dear Amber experts,
I am on the process of deriving point charges for a small molecule of 51 atoms. From is SMILES string, I’ve generated several conformers using RDKit (
http://www.rdkit.org/). My objective is to do multi-conformational RESP fitting. I’ve seen on the Advanced Tutorial1
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm that the recommended way to do this for reproducibility is using the R.E.D server. However I decided to manually do it myself too to better understand the process.
Starting from 9 conformers, I’ve noticed that some of them are differ in energies (between 3 to 10 kcal/mol to the lowest energy conformer, Gaussian SPE calculation and M06/cc-pvdz). Should I only use for resp the conformers that are around < 2kcal/mol to the lowest energy conformer? I think this can be also done by tweaking with the weighting factor for the multi-molecule fit. But in the tutorial, it just states that is set to 1.0 for both conformers since the two have to be weighted equally. I’ve been looking in the manual and haven’t seen much being discussed about this weighting factor. Does anyone know how to use it to better represent the energy difference between the conformers?
Additionally, and this is related to the R.E.D server: is it possible to modify these weighting factors according to the energy difference between the conformers (after optimization, presumably)? I’ve set up a job with 9 conformers of the molecule in a single PDB file, but upon inspection of the job results, I’ve observed that these weighting factors are all set to 1.0. I’ve also noticed that the input file for resp in the R.E.D server doesn’t set the nmol keyword to however many conformers there are – instead, on top of every molecule section something like this is set: MOLECULE-1 nconf=1 norient=1 nmep=1/18 (the nconf, norient and nmep values change). Can anyone comment or point me in the right direction to better understand the input files for resp? I’m also a bit confused by the fact that there are 18 entries in this resp input file when I only loaded 9 conformers.
Thanks for any suggestions!
Juan Eiros
[Imperial College London] <
http://www.icb-cdt.co.uk/>
Juan Eiros Zamora / PhD Student
je714.ic.ac.uk<mailto:
je714.ic.ac.uk> / +44 (0) 7783018326
Imperial College London
Imperial College Road SW7 2AZ | UK
http://www.icb-cdt.co.uk/
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Received on Tue Jun 06 2017 - 04:30:03 PDT
