AMBER Archive (2009)

Subject: [AMBER] RE: charge not zero on group:''''.respin1 attached

From: Jio M (jiomm_at_yahoo.com)
Date: Sat Jul 18 2009 - 09:40:18 CDT

Dear AMBER users,
               
Thanks BEN for the reply but I didnt understand fully what you
suggested. Now I have attached .respin1 file also {note I have removed
one blank line space as it was suggested in archive}

>I am trying to give net charge on terminal group(--COCH3) to
>bezero,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


_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber