[AMBER] Use leaprc.ff99SB force field

From: Jan Wahl <janwahl.gmx.de>
Date: Fri, 14 Jan 2011 15:21:34 +0100


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
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