Dear,
We had properly compile amber 6 under RH 6.1 using pgroup compiler ver
3.1.
We tried to repeat, with sander 6, an energy minimization using NOE
constraints already done with sander 5 for a protein of 73 residues.
We used the following input file for amber 5 and it works fine.
-------------------------------------------------
Cu-ATX1 (RMIN on DIANA files
&cntrl
ibelly=0,imin=1,nrun=0,nsnb=10,ntpr=100,
ntwx=100,ntwe=100,ioutfm=0,ntr=0,maxcyc=6000,
ncyc=1500,ntmin=1,dx0=0.0001,dxm=1.0,dele=1.0e-07,
drms=.2,cut=10.,idiel=0, scee=2.0,
nmropt=1,pencut=0.1, ipnlty=2
&end
&wt type='REST', istep1=0,istep2=1,value1=0.,
value2=1.0, &end
&wt type='END' &end
DISANG=../noe/noe.in
LISTOUT=POUT
--------------------------------------------------
Before running sander 6 we changed the input file according to the
manual chapter 6.3 of the SANDER module as indicated below.
The program works properly without NOE (nmropt=0), on the contrary if
nmropt=1 the program crashes creating a core file.
The same thing occurred with sander_classic using the first input file.
--------------------------------------------------
Cu-ATX1 (RMIN on DIANA files
&cntrl
ntb=0,igb=3,
ibelly=0,imin=1,nsnb=10,ntpr=100,
ntwx=100,ntwe=100,ioutfm=0,ntr=0,maxcyc=6000,
ncyc=1500,ntmin=1,dx0=0.0001,dxm=1.0,dele=1.0e-07,
drms=.2,cut=10.,scee=2.0,
nmropt=1,pencut=0.1, ipnlty=2,
&end
&wt type='REST', istep1=0,istep2=1,value1=0.,
value2=1.0, &end
&wt type='END' &end
DISANG=../noe/noe.in
LISTOUT=POUT
------------------------------------------------------
Any idea? HELP US PLEASE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Best regards
-------------------------------- /\\\\\\
Enrico Morelli /\|||||||
---- /__ __ ::;
CE.R.M. | O O _
CEntro Risonanze Magnetiche / | |
--- |_/ _|
Tel : +39 055 4209269 |_/ |
Fax : +39 055 4209253 | /
e-mail: morelli_at_cerm.unifi.it / _/
http://litio.cerm.unifi.it/~morelli \_ /
-------------------------------------------
Centro di Risonanze Magnetiche
Polo Scientifico - Universita' di Firenze
Via Luigi Sacconi, 6
50019 Sesto Fiorentino (FI)
--------------------------------------------
Received on Fri Apr 14 2000 - 03:02:54 PDT
