AMBER Archive (2007)

Subject: AMBER: solvateCap minin and mdin for qm-mm dftb

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Aug 24 2007 - 05:19:30 CDT


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

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