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AMBER Archive (2009)Subject: [AMBER] -a flag :RESP
From: Jio M (jiomm_at_yahoo.com)
Dear AMBER users,
I didnt find tutorial for AMBER10 to make group charge to be zero.
As I have used -a flag for preparing .respin1 file I didnt get group
but when I used -a flag two times, that is for .respin1 and .respin2, I got group charge zero
residue is NH2-CH2CH2-NH--COCH3 (-COCH3 group charge needs to be zero). but once we defined COCH3 group charge to be zero in .respin1 file why to use -a flag again for .respin2
the .in file contains
GROUP 6 0.00000
ATOM 12 C3
ATOM 13 O1
ATOM 14 C4
ATOM 15 H8
ATOM 16 H9
ATOM 17 H10
following commands were used
respgen -i eda_v_esp.ac -o eda.respin1 -f resp1 -a eda_v.in
respgen -i eda_v_esp.ac -o eda.respin2 -f resp2 -a eda_v.in
resp -O -i eda.respin1 -o eda.respout1 -e eda_v.esp -t qout_stage1
resp -O -i eda.respin2 -o eda.respout2 -e eda_v.esp -q qout_stage1 -t qout_stage2
antechamber -i eda_v_esp.ac -fi ac -o eda_1.mol2 -fo mol2 -c rc -cf qout_stage2
somebody pls help as no such tutorial I have found for AMBER 10 to make group charge to be zero.
thanks
Jiomm
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