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Dear Amber Users,
The molecule I am using for simulation contains two Selenium atoms (viz. Se1 and Se2). For setting “Se” as an atom type I have used following commands:
***************************************** >addAtomTypes { {"Se1" "Se" "sp2"} } addAtomTypes: type Se1 - max length is 2
> addAtomTypes { {"Se2" "Se" "sp2"} } addAtomTypes: type Se2 - max length is 2 ****************************************Than to set partial charges for the atom which I have these commands: **************************************** > s1=createAtom Se1 Se 0.37744 > s2=createAtom Se2 Se 0.32396 **************************************** and to set element following commands **************************************** > set s1 element Se > set s2 element Se **************************************** My questions are- 1. Is this a correct way to add an atom? 2. How to set atomic radius for Se atom? Because when I add solvent in the system It is giving following output: > solvateoct c TIP3PBOX 8 (using default radius 1.500000 for Se1) (using default radius 1.500000 for Se2) Scaling up box by a factor of 1.159796 to meet diagonal cut criterion Solute vdw bounding box: 44.319 22.848 42.645 Total bounding box for atom centers: 62.876 62.876 62.876 (box expansion for 'iso' is 56.0%) Solvent unit box: 18.774 18.774 18.774 (using default radius 1.500000 for Se1) (using default radius 1.500000 for Se2) Volume: 130310.325 A^3 (oct) Total mass 66695.892 amu, Density 0.850 g/cc Added 3240 residues. 3.What is the correct value for Se radius? |