Dear Marc, the adequacy in use semi-empirical charges for MD simulations depends on the structure of the compound to be simulated. For example, compounds presenting sulphur or phosphorus in its oxidized forms are not well described by semi-empirical methods due to the absence of d orbitals in the calculations (do not use MNDO/d method, since it does not present any improve in description of organic molecules). Another point that is frequently raised when using atomic charges from quantum methods in MM studies regards to the used atomic charge scheme. Generaly charges derived from the molecular electrostatic potential are better then Mulliken derived charges. However, properties based on electrostatic potential are highly dependent on the molecular conformation (so choose carefully the conformation to derive the charges). These two schemes of atomic charges can be obtained with semi-empirical methods. An aditional method is the Lowdin scheme, that while is much less dependent on molecular conformation than the electrostatic potential derived charges, is highly correlated with it (Becker et al, Carbohydr. Res. 340, 2005, 1499-1507).
If you are not intended to perform simulations with sulphate or phosphate groups, semi-empirical charges should work fine. Try to use RM1 semi-empirical method (Rocha et al, J. Comp. Chem. 27, 2006, 1101-1111, http://www.rm1.sparkle.pro.br/), much better than PM3 and possibly than PM5, but free. If not, is better to use ab initio derived charges (you can minimize the molecule with 3-21G basis set and further perform a single point calculation with 6-31G** basis set, for example). Additionally, you should have in mind that the properties of a molecule in a MD simulation with solvent and/or protein are not equally dependent on the atomic charge. For example, we compared different basis sets on its abilities to reproduce polysaccharide geometry in solution (Becker et al, Carbohydr. Res. 340, 2005, 1499-1507). We observed that the modification of the atomic charge scheme does not interfere in the molecular geometry, but it does modify the interaction energy with the surrounding medium (solvent or protein). However, it does not prevent you to observe relevant biological phenomena, as ligand induced conformational changes (Verli & Guimarães, J. Mol. Graph. Mod. 24, 2005, 203-212). If you use the same protocol to obtain the atomic charges, probably the error associated with the charges will be linearized. I hope this helps. Best regards, Hugo Verli. > Hey all, > > I would appreciate an opinion on this. Is it acceptable to caluclate > partial charges using a semi-empirical method (PM3) for topologies obtained > frmo PRODRG? Is there any vital information that gets missed or skewed by > doing this? I have noticed that some QM/MM strategies will use > semi-empirical methods for the QM side of the analysis and so was wondering > if the same rationale can be applied to the caluclation of partial charges, > or is this an apples to oranges type of comparison? > > Regards, > > Marc > Prof. Hugo Verli Departamento de Produção de Matéria Prima Faculdade de Farmácia - UFRGS Av. Ipiranga 2752, Porto Alere, RS CEP 90610-000, Brasil tel.: +55 51 3316 7770 +55 51 3316 5526 -------------------------------------------------------------------- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
