On Thu, Mar 01, 2018, M Conte wrote:
>
> *PDB file*
>
> ATOM 1 S SO2 1 4.853 -7.956 1.549 1.00 1.5000 s6
> ATOM 2 O1 SO2 1 3.488 -7.383 1.304 1.00 1.5000 o
> ATOM 3 O2 SO2 1 5.870 -6.854 1.535 1.00 1.5000 o
> TER
> END
> CONECT 1 2 3
> CONECT 2 1
> CONECT 3 1
>
You need to run this through antechamber and parmchk2 first, to create
SO2.mol2 and SO2.frcmod files. Then load those into tleap, before you
load the pdb file.
Explanation: loading gaff.dat just loads force field parameters: you
also need to load Amber libraries (i.e. mol2 or off files) that describe
all the residues/molecules in your system.
(Aside: pdb files are column-oriented, so you need to fix ATOM 1 in the
PDB above.)
....good luck...dac
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Received on Mon Mar 05 2018 - 05:30:03 PST
