On Friday 07 January 2005 09:51 am, Cenk Andac wrote:
> 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?
>
The restart file for a coupled potential run is (very slightly)
different from an ordinary MD restart file (has to have
coordinates for the link atoms in it). You need to do a coupled
potential MINIMIZATION (1 cycle is sufficient to satisfy the
software, and may even be sufficient in other aspects if the
structure is already well relaxed with respect to the FF) to
generate an appropriate restart file. Then use the restart file
from the minimization run as the starting structure for the
coupled potential MD run.
> 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.
>
>
It might be better to describe to the list what you are trying to
accomplish and get knowledgeable comments. Coupled potential runs
are quite "tricky" to setup and interpret, in my experience.
Bud Dodson
--
M. L. Dodson bdodson.scms.utmb.edu
409-772-2178 FAX: 409-747-8608
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Received on Fri Jan 07 2005 - 16:53:00 PST
