[16-VII-2012]
Hi Everybody,
I would like to run some tests for a Free Energy Calculation using Termodynamic Integration (TI) and softcore potentials in sander (amber11).
I have prepared my input files (coordinates and topology) for states 0 and 1 with LEaP following the information given in Tutorial A9 (in amber tutorials webpage). I have also been reading the Amber11 manual about TI and sander. Then, when reading the different flags/options for "ifsc" it says that you have to select ifsc=1 to activate the softcore potentials BUT it also continues with:
"Note that a different setup is required, so prmtop files for non soft core simulations cannot be used with soft core potentials and vice versa".
I have been reading also LEaP info at AmberTools11 manual but I have not found any remark about this...
I thought that the parmtop files for MD calculations were basically compatible with TI calculations. Can anyone tell me what are the differences between the parmtop files for non-SC potentials / SC potential simulations? Then, how should I proceed to create the parmtop files with LEaP for TI and SC potentials?
Thank you very much.
Kepa K.
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Received on Mon Jul 16 2012 - 12:00:02 PDT
