AMBER Archive (2005)

Subject: Large files to AMBER, RE: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation.

From: Yong Duan (duan_at_ucdavis.edu)
Date: Wed Apr 20 2005 - 10:16:55 CDT

Dear Zhli,
 
AMBER mail reflector is used by thousands and many perhaps use dial-up
modems or the equivalents (particularly on the road). Loading a piece of
1MB mailthrough those slow connections is not a fun thing. So, please
try not to send large attachment to the reflector. Instead, in your
case, if you like to share the information with Ross, you are welcome to
send the files to him :).
 
 
yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of zhli_2000
Sent: Wednesday, April 20, 2005 6:52 AM
To: amber_at_scripps.edu
Cc: ross_at_rosswalker.co.uk
Subject: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after
minimisation.

Dear Ross,
First,I'm sorry this reply was delayed. I had thought this letter had
been sent successfully on 19 Apr., but I found it didn't seem so today.
So I sent this letter again.
Thank you for advice. The following is the process to create the prmtop
and inpcrd files:
source leaprc.ff99
mod=loadamberparams FAD.frcmod
loadamberprep FAD.prep
mod=loadamberparams TEM.frcmod
loadamberprep TEM.prep
mod=loadamberparams TON.frcmod
loadamberprep TON.prep
source leaprc.gaff
RL=loadpdb ppo_cyc_4_opposite.pdb
saveamberparm RL ppo_cyc_4_o_noWT.top ppo_cyc_4_o_noWT.crd

And you will find the output files from the minimisation in the
attachment.
Thanks again.
Best wishes!
Zhli

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