Dear amber users,
Though this might be very minute issue but it has been bothering for some time and I hope someone can explain it
As far I have understood geometry optimization is considered important for molecular dynamics and can done by empirical or semiempirical like sqm methods.
Now my query is when is sqm invoked as a result of antechamber by using the command "antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc 0" what is true purpose? Is it just to derive AM1-bcc charges or it does geometry optimisation too?
Also after this command we get ligand.mol2 file and also sqm.pdb file. Which file should be used for further process like merging with protein to protein-receptor complex etc? if sqm.pdb is the right choice for file to be used then I have to convert it into .mol2 format again as parmchk don't read .pdb files as input files.
As the default option for bcc charge calculation is sqm then how come sometimes I find mopac. Are there specific conditions in which sqm or mopac are used?
I apologize if this question seems to irrelevant BUT I hope for an answer.
Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
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Received on Fri Feb 14 2014 - 00:00:02 PST
