AMBER Archive (2009)

Subject: [AMBER] charge not zero on group: RESP

From: Jio M (jiomm_at_yahoo.com)
Date: Sat Jul 18 2009 - 00:14:58 CDT

Dear AMBER users,

I am trying to give net charge on terminal group(--COCH3) to be
zero,being capped on residue's N terminal (is it correct to do like this
if not pls correct me):

                                    
NH2-CH2CH2-NH--COCH3

1) I optimised capped residue with hf/631+ g( d ) also esp derived on same basis and got eda_v.esp (sorry I cant attach this file : it cross the limit of mail size 2083 kb)

2) I read in archive that .respin1 and .respin2 files should be
corrected by removing blank line.I corrected it also for .respin1

3) I have constrained the group charge to be zero by eda_v.in file (pls try to have a look on it)

4) but I am not getting net charge on --COCH3 to be zero, though net charge on residue is zero

5) reason can be that I am using only one conformation; but I think it
should not matter because I am using constraint on group charge to be
zero (pls correct me)

I used following with -a flag :

respgen -i eda_v_esp.ac -o eda_v.respin1 -f resp1 -a eda_v.in

gedit eda_v.respin1

respgen -i eda_v_esp.ac -o eda_v.respin2 -f resp2

resp -O -i eda_v.respin1 -o eda_v.respout1 -e eda_v.esp -t qout_stage1

resp -O -i eda_v.respin2 -o eda_v.respout2 -e eda_v.esp -q qout_stage1 -t qout_stage2

antechamber -i eda_v_esp.ac -fi ac -o eda_v.mol2 -fo mol2 -c rc -cf qout_stage2

pls suggest the missing things or this method cannot be used at all

thanks

Jiomm



  • application/octet-stream attachment: eda_v.in

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