AMBER Archive (2004)

Subject: AMBER: sander8

From: Vincent Bisetty (bisettyk_at_dit.ac.za)
Date: Fri Oct 08 2004 - 09:59:01 CDT

Hi,
(Thanks Ross for your prompt replies to all my previous messages-the MD
simulations are up and running in amber8 )...My problem now is
converting my files from amber5 to amber8.
I previously used amber5 to calculate the energies of the backbone
torsional angles (phi and psi) on my cage peptides, and the minimization
worked fine for me. Now that Iam working in amber8, the inputs are
different. I tried various options, without any luck.
Below is my sander input files for amber5 & amber8. Please have a look
and any suggestions would be greatly appreciated.
regards,
vincent.

Sander input file amber5
acc
 &cntrl imin=1, maxcyc=4400, nrun=0, nsnb=50, idiel=1, cut=8.0,
nmropt=1,
 scee=1.2,
 &end
 &wt type="END", &end
 &rst iat(1)=5, iat(2)=7, iat(3)=9, iat(4)=32,
 r1=-210, r2=-180, r3=-180, r4=-150,
 rk2=50.0, rk3=50.0, &end
 &rst iat(1)=7, iat(2)=9, iat(3)=32, iat(4)=34,
 r1=-210, r2=-180, r3=-180, r4=-150,
 rk2=50.0, rk3=50.0, &end
 &rst iat=0
>>>>>>>>>>>>>>>>>>>>

amber8 (rst.f)
&rst iat= 5,7,9,32, r1=-210,
      r2=-180, r3=-180, r4=-150, /
 &rst iat=7,9,32,34, r1=-210,
      r2=-180, r3=-180, r4=-150, /
 &rst iat=0 /

>>>>>>>>>>>>>>>>>>>>>>>
amber 8 min.in
acc
 &cntrl
  imin=1, maxcyc=4400, dielc=1, cut=8.0,
  scee=1.2, nmropt=1,
/
LISTOUT=POUT
DISANG=rst.f
/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
regards,
vincent. 

--

Dr K Bisetty
Senior Lecturer 
Department of Chemistry
Steve Biko Campus
Durban Institute of Technology
P O BOX 1334
Durban
4000
Tel : +27-031-2042311
Fax : +27-031-2022671
"ND-4-SPD"
bisettyk_at_dit.ac.za

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