AMBER Archive (2004)

Subject: Re: AMBER: A Question about RESP

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Sat Mar 06 2004 - 07:31:51 CST

Hi,

Try this:

antechamber -i new.out -fi gout -o new.ac -fo ac

espgen -i new.out -o new.esp

respgen -i new.ac -o new.respin1 -f resp1
respgen -i new.ac -o new.respin2 -f resp2

(at this step, you might want to modify respin1 and respin2, e.g. restrain
your backbone, etc)

resp -O -i new.respin1 -o new.respout1 -e new.esp -t qout_stage1
resp -O -i new.respin2 -o new.respout2 -e new.esp -q qout_stage1 -t
qout_stage2

antechamber -i new.ac -fi ac -o new_resp.ac -fo ac -c rc -cf qout_stage2
antechamber -i new_resp.ac -fi ac -o new.prep -fo prepi

Hope it helps,
Bimo

> Hi all,
> I am going to create a new type of residue to run MD. Antechamber is
> the only tool I can use so far in Amber 7. However, when I type the
> following command:
>
> antechamber -i new.out -fi gout -o new.prepin -fo prepi -s 2 -nc -2
> -at amber -c resp
> (new.out is the output file created by Gaussain 98, single point
> calculation)
>
> The responce which Amber showed me was:
>
> Running: /usr/local/amber7/exe/espgen -o ANTECHAMBER.ESP -i new.out
> Running: /usr/local/amber7/exe/respgen -i ANTECHAMBER_RESP.AC -o
> ANTECHAMBER_RESP1.IN -f resp1
> Running: /usr/local/amber7/exe/respgen -i ANTECHAMBER_RESP.AC -o
> ANTECHAMBER_RESP2.IN -f resp2
> Running: resp -O -i ANTECHAMBER_RESP1.IN -o ANTECHAMBER_RESP1.OUT -e
> ANTECHAMBER.ESP -t qout
> Unit 5 Error on OPEN: ANTECHAMBER_RESP1.IN
> resp -O -i ANTECHAMBER_RESP2.IN -o ANTECHAMBER_RESP2.OUT -e
> ANTECHAMBER.ESP -q qout -t QOUT
> Unit 5 Error on OPEN: ANTECHAMBER_RESP2.IN
> Cannot open QOUT , exit
>
> I checked the process step by step and when I execute espgen, there
> was nothing happened. No messages and no output files. But it's OK to
> run respgen. Could someone understand what's going on and tell me how I
> can run ANTECHAMBER correctly. Thanks.
>
> Ming-Hsun Ho 

-- 
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