Dear amber community,
I will have two questions regarding
sander.QMMM
1) I was wondering if it is possible to run
sander.QMMM using NOE restraints.
I added a solvatecap around the center of my molecule
in xleap as follows
>solvatecap MOL TIP3PBOX MOL.MOL.O1 15 0.7
>Center of solvent box is:
-5.456166, -10.706805, -8.113191
>Added 400 residues.
>saveamberparm MOL MOL.prmtop MOL.x
I checked my unit in xleap and it gave no errors.
Then I relaxed my MOL using sander.QMMM with the
following
divcon.in and relax.in parameters:
divcon.in :
CARTESIAN PM3 CHARGE=4 &
STANDARD DIRECT
END_COORD
relax.in:
&cntrl
imin=1, maxcyc=500, ncyc=250,
cut=20, ntb=0, fcap=1.5,
ifqt=1, nqt=52, idc=0,
/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27
28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51
52
END
END
which gave no errors during relaxation.
However, I encountered a problem when
I tried to run sander.QMMD with the following
input parameter which requires use of NOE
restarints. Of course, I carried out the second
sander.QMMM run for relaxed coordinates.
qmmm.in:
300K constant temp QMMM
&cntrl
imin=0, ntb=0, pencut=-0.001,
cut=20, fcap=1.5,
tempi=0, temp0=300.0,
ntt=3, gamma_ln=10, vlimit=10,
nstlim=1000, dt=0.001,
ntpr=10, ntwx=10, nmropt=1,
ifqt=1, nqt=12, idc=0,
/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27
28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51
52
/
&wt type='REST',
istep1=0,istep2=500,
value1=0.1, value2=1.0, /
&wt type='REST',
istep1=501,istep2=1000,
value1=1.0, value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=RST33gg-2
END
END
Consequently I received the following error message
in qmmm.out file
Number of triangulated 3-point waters found: 400
FATAL ERROR
Link atoms MUST be optimized before MD run
Could anyone please let me know how to optimize the
link
atoms or let me know if there is anything wrong with
my
input parameters?
2)Is it a good idea to incorporate NOE restraints
during
QMMM runs for solvated systems? Would it be a better
idea
to NMR restrain my molecule in implicit water first,
then
take the final structure of my molecule, solvate it
and run
sander.QMMM putting a restrain for the final
structure?
3) Is it possible to score final QMMM structures using
mm_pbsa?
As far as I understand from the QMMM tutorial (2004),
a solvatebox
is not added in prmtop files. I have tried running
mm_pbsa for an
QMMM coordinate output, however, mm_pbsa was unable to
execute pbsa.
Do I need to define a solvatebox in my prmtop file
while running
sander.QMMM so that mm_pbsa will be ok with
sander.QMMM output.
cheers,
jenk.
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Received on Fri Jan 07 2005 - 16:53:00 PST
