Dear Amber users,
I have a protein with bound substrate which is phenyl ring with two chlorines attached to it. Chlorine have atom name: CLAM and CLAN
Using Antechamber I made frmod, prepin and lib file for it. I was able to generate inpcrd and prmtop file for the ligand. But when I run the xleap using:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
and then
source leaprc.gaff
loadamberprep substrate.prepin
loadamberparams substrate.frcmod
loadoff substrate.lib
and load protein in complex with the substrate.
while building the topology it is giving error:
FATAL: Atom .R.A does not have a type.
FATAL: Atom .R.A does not have a type.
Failed to generate parameters
Parameter file was not saved.
I dont know why it is not able to recognise the Chlorine atom even after loading lib and frcmod file.
Kindly Help.
Regards
Shivu
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Received on Wed Dec 25 2013 - 22:00:02 PST
