Hello,
after having some problems in the begining of using AMBER 11 i was able to do my calculations .
But now i have some new problems :
i did all my calculations with the default force field LEAPRC.GAFF
but now i wanted to do some calculations with differnet force fields e.g ff99SB. therefore i used again my .mol2 file to create a prmtop using antechamber :
antechamber -i input.mol2 -fi 2 -o in.mol2 -fo 2
and pamrchk :
parmchk -i ANTECHAMBER_AC.AC -f ac -o frctop
using tleap
source leaprc.ff99SB
.
.
.
saveAmberParm (unit) prmtop inpcrd
using these commands i was not able to save a prmtop.
The manual told me to use the flag -at in antechamber and with this command i was able to create a prmtop.
To check the results i did a calculation using the same structure but now i used a pdb-file to create the prmtop.
after the calculation the result is different from the result using a mol2 file.
Where is my error?? what am i doing wrong??
Thank you fr your help
Jan Wahl
Goethe University/ Germany
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Received on Fri Jan 14 2011 - 06:30:02 PST
