Hi, dac:
Thanks for your mail.
I am using AMBER 11, I am not sure does that tell you which version of
sander I am using. If not, please guide me to get the sander version
information.
Here following are all the using commands and the input files.
Best,
backy
====================================================
print `tleap -f leapin\n`;
leapin:
source /netapp/sali/AMBER/amber11/dat/leap/cmd/oldff/leaprc.ff03
set default PBradii bondi
trx = loadpdb 1a4y-A-minimize.pdb
saveamberparm trx 1a4y-A.prmtop 1a4y-A_rec.crd.1
quit
====================================================
print `sander -O -i sander2.in -p 1a4y-A.prmtop -c 1a4y-A_rec.crd.1 -ref
$1a4y-A_rec.crd.1 -o 1a4y-A.out -r 1a4y-A.res \n`;
sander2.in
File generated by mm_pbsa.pl. Using MM GB MS
&cntrl
ntf = 1, ntb = 0, dielc = 1.0,
idecomp= 2,
igb = 2, saltcon= 0.00,
offset = 0.09,
intdiel= 1.0, extdiel= 80.0,
gbsa = 2, surften= 1.0,
cut = 999.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 1, ncyc = 0,
&end
END
END
======================================================
On Tue, Feb 15, 2011 at 6:08 AM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Feb 14, 2011, Yao-Chi Chen wrote:
> >
> > I run a one-step sander calculation, but the strange thing is: the ESURF
> > terms of the following results are different though the difference is
> quite
> > small. What happened?
>
> I can't reproduce this behavior in my test cases. Which version of sander
> are
> you using? Can you send the input files?
>
> ...thx...dac
>
>
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Received on Tue Feb 15 2011 - 10:30:02 PST
