I am trying to build prmtop and inpcrd for qm-mm with theory=7 (dftb). I am
stuck at solvateCap, argument #3 (position).
Using *.prepin and *frcmod from previous successful runs with theory=2,
startx
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmod/leaprc.ff99
source leaprc.gaff
loadamberprep EQE.prepin
loadamberparams EQE.frcmod
check EQE (unit is OK)
solvateCap EQE TIP3PBOX EQE 20.0
returns
Argument #3 is type Unit must be of type: [molecule residue atom list]
Using as Argument #3: "1" (residue number in prepin), "C17" (a central carbon
atom number in prepin, "c" the C17 atom type, or, finally (and blindly)
EQE.2.CA the error is: Argument #3 is type String.
I am short of imagination (even consulting the manual and the mailing list) of
what should be given in my case as Argument #3.
________________--
That said, on summing up info from the manual and suggestions from Bud and
Gustavo, I have a number of doubts about min.in and md.in, in particular if
qm_pme should be omitted at all. The two files I have set up read:
Initial min for qmmm with dftb
&cntrl
imin=1, maxcyc=500, ncyc=200,
cut=20.0, ntb=1, ntc=2, ntf=2,
ivcap=0, fcap=10
ifqnt=1
/
&qmmm
qmmask=':1',
qmcharge=0,
qmtheory=7,
qmshake=0,
qm_ewald=0
/
300K constant temp for qmmd with dftb
&cntrl
imin=0, ntb=1
cut=20.0, ntc=2, ntf=2,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
nstlim=20000, dt=0.002,
ivcap=0, fcap=10,
ntpr=100, ntwx=100,ifqnt=1
/
&qmmm
qmmask=':1',
qmcharge=0,
qmtheory=7,
qmshake=0,
qm_ewald=0
/
I want to try if, at the current implementation of qm-mmm/dftb in Amber9, speed
is acceptable for a 98-atoms molecule. If acceptable, to compare ESCF and EPtot
with AM1.
Thanks for checking
francesco pietra
____________________________________________________________________________________
Luggage? GPS? Comic books?
Check out fitting gifts for grads at Yahoo! Search
http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 26 2007 - 06:07:38 PDT
