[AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file

From: onetwo <twoone21.rediffmail.com>
Date: 26 Dec 2013 05:57:20 -0000

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.


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Received on Wed Dec 25 2013 - 22:00:02 PST
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