Hi,
I have a mol2 file and a frcmod file (attached) that i recently used to
simulate a surface. the simulation runs so the prmtop file and inpcrd
files are okay, however if i try and create a pdb file from the output
files, ambpdb -p surf.prmtop <surf.res> surf.pdb the structure (bonds)
and some of the atoms are incorrect. So i tried this
xleap
source leaprc.gaff
loadamberparams mysioforce.frcmod
surf = loadmol2 SiO2APTMS.mol2
edit surf --it looks right
saveamberparm surf surf.prmtop surf.inpcrd
outside xleap
ambpdb -p surf.prmtop <surf.inpcrd> surf.pdb
the file surf.pdb is not the same as the original mol2 file, some Si
atoms are labeled L and the bonds are all gone. i tried ambpdb -bres
option, and the outcome is the same.
it is important to create a pdb or a mol2 file of the (surf.prmtop
surf.rst output) correctly, i am not sure how.
Received on Wed Mar 18 2009 - 01:12:05 PDT
