AMBER Archive (2009)

Subject: [AMBER] -a flag :RESP

From: Jio M (
Date: Sun Jul 19 2009 - 05:48:20 CDT

Dear AMBER users,

I didnt find tutorial for AMBER10 to make group charge to be zero.
 I have a query regarding use of -a flag in respgen.. can we use it in respin1  as well  as  respin2?

As I have used -a flag for preparing .respin1 file I didnt get group
charge in residue to be zero (constrained group charge defined by .in
file used by -a flag)

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 -o eda.respin1 -f resp1 -a

respgen -i -o eda.respin2 -f resp2 -a

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 -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.



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