Hi Jani,
I would highly recommend upgrading to AMBER 11. If you want to use AMBER 10
then you'll need to edit the qmmm_module.f file in $AMBERHOME/src/sander/ so
that it can recognize the entire periodic table rather than just the atomic
numbers recognized but the PM3, AM1, MNDO semi-empirical Hamiltonians.
All the best
Ross
> -----Original Message-----
> From: jani vinod [mailto:genomejani.gmail.com]
> Sent: Wednesday, October 12, 2011 5:52 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] regarding qmmm simulation
>
> Dear Ross,
> Thanks for the reply.
> I have already checked MASS section the is around 58. Actually I am
> using
> amber 10.
> Is there any to fix it up for amber 10.
>
>
>
> On Tue, Oct 11, 2011 at 9:36 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Jani,
> >
> > I am assuming you are using AMBER 11 + AmberTools 1.5 with the latest
> > bugfixes. In this case the relevant source code is
> > $AMBERHOME/AmberTools/src/qmmm_module.f with the routine:
> >
> >
> !++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> +
> > !+Identify qm atom elements.
> > subroutine get_atomic_number(atom_name,atom_mass,atomic_number)
> > !
> >
> > ...
> > ...
> >
> > !Nobel Gasses are not supported.
> > !Lanthanides are not supported.
> > !Actinides are not supported.
> >
> > if(atom_name(1:1) .eq. 'a' .or. atom_name(1:1) .eq. 'A') then
> > if(atom_mass > 24.0d0 .and. atom_mass <= 28.0d0) then
> > atomic_number = 13 !Aluminium
> > ...
> > ...
> > ... and the critical section for you ...
> > elseif(atom_name(1:1) .eq. 'c' .or. atom_name(1:1) .eq. 'C') then
> > if(atom_mass > 10.0d0 .and. atom_mass <= 14.0d0) then
> > atomic_number = 6 !Carbon
> > elseif(atom_mass > 33.0d0 .and. atom_mass <= 37.0d0) then
> > atomic_number = 17 !Chlorine
> > elseif(atom_mass > 38.0d0 .and. atom_mass <= 42.0d0) then
> > atomic_number = 20 !Calcium
> > elseif(atom_mass > 50.0d0 .and. atom_mass <= 54.0d0) then
> > atomic_number = 24 !Chromium
> > elseif(atom_mass > 57.0d0 .and. atom_mass <= 61.0d0) then
> > atomic_number = 27 !Cobalt
> > elseif(atom_mass > 61.0d0 .and. atom_mass <= 65.0d0) then
> > atomic_number = 29 !Copper
> > elseif(atom_mass > 110.0d0 .and. atom_mass <= 114.0d0) then
> > atomic_number = 48 !Cadmium
> > elseif(atom_mass > 131.0d0 .and. atom_mass <= 135.0d0) then
> > atomic_number = 55 !Cesium
> > else
> > write(6,*) 'Unable to correctly identify element ',
> atom_name
> > call mexit(6,1)
> > endif
> >
> > Note if the atomic mass is between 57 and 61 it will identify the
> element
> > as
> > cobalt. What is the atomic mass of the cobalt in your prmtop file?
> >
> > I would also make sure that Xleap itself identified the atom as
> cobalt and
> > gave it the correct VDW parameters and atomic mass. My betting is
> that leap
> > thinks it is a carbon - So you should probably check this first -
> find the
> > cobalt in your prmtop file and find it's mass in the MASS section of
> said
> > file.
> >
> > If you are using AMBER 10 and/or AMBERTools 1.4 or earlier then you
> will
> > almost certainly need to upgrade.
> >
> > All the best
> > Ross
> >
> > > -----Original Message-----
> > > From: jani vinod [mailto:genomejani.gmail.com]
> > > Sent: Tuesday, October 11, 2011 5:30 AM
> > > To: AMBER Mailing List
> > > Subject: [AMBER] regarding qmmm simulation
> > >
> > > Dear All,
> > > I am trying to simulate a enzyme-ligand complex where ligand is
> > > cobalt-complex.I am trying to carry out DFTB type QMMM simulation.
> > > I have also downloaded trans3d parameters from dftb and placed them
> in
> > > slko
> > > directory. Now when I am trying to run qmm simulation keeping my
> ligand
> > > in
> > > QM part Sander is treating Cobalt as carbon and Carrying out
> > > simulation.This I came to know from log file where in QM region
> first
> > > atom
> > > was show as carbon (part of output is pasted below) In prmtop file
> the
> > > atom
> > > name of cobalt is mentioned as CO1 and amot type as Co.
> > >
> > > Part of my prmtop is pated below
> > >
> > > %FLAG ATOM_NAME
> > > *CO1* N1 C1 H1 C2 H2 C3 H3 C4 C5 C6 N3 H3A N2 H2A C7
> O1
> > > N11
> > > C11 H11 C21 H21
> > > C31 H31 C41 C51 C61 N31 H3A1N21 H2A1C71 O11 N12 C12 H12 C22 H22 C32
> H32
> > > C42
> > > C52
> > > C62 N32 H3A2N22 H2A2C72 O12 N13 C13 H13 C23 H23 C33 H33 C43 C53 C63
> N33
> > > H3A3N23
> > > H2A3C73 O13 N14 C14 H14 C24 H24 C34 H34 C44 C54 C64 N34 H3A4N24
> H2A4C74
> > > O14
> > > N15
> > > C15 H15 C25 H25 C35 H35 C45 C55 C65 N35 H3A5N25 H2A5C75 O15 O H1
> H2
> > > O
> > >
> > > %FLAG AMBER_ATOM_TYPE
> > > %FORMAT(20a4)
> > > *Co* NA CA HA CA HA CA HA CA CA CT N H N H C
> O
> > > NA
> > > CA HA CA HA
> > > CA HA CA CA CT N H N H C O NA CA HA CA HA CA
> HA
> > > CA
> > > CA
> > > CT N H N H C O NA CA HA CA HA CA HA CA CA CT
> N
> > > H
> > > N
> > > H C O NA CA HA CA HA CA HA CA CA CT N H N H
> C
> > > O
> > > NA
> > >
> > >
> > > *output is pasted below where in output first atom should be cobalt
> > > where it
> > > is being treated as C*
> > > Output
> > > QMMM: QM_NO. MM_NO. ATOM X Y Z
> > > * QMMM: 1 8279 C -0.6382 -0.6715 0.9812*
> > > QMMM: 2 8280 N 1.2731 -0.6218 -0.0952
> > > QMMM: 3 8281 C 1.9976 0.3551 -0.8670
> > > QMMM: 4 8282 H 1.5998 1.3182 -1.1764
> > > QMMM: 5 8283 C 3.3121 0.2335 -1.2932
> > > QMMM: 6 8284 H 3.7125 1.0319 -1.9127
> > > QMMM: 7 8285 C 4.0161 -0.9201 -1.0509
> > > QMMM: 8 8286 H 4.9968 -1.0257 -1.5078
> > > QMMM: 9 8287 C 3.4570 -1.8830 -0.2573
> > > QMMM: 10 8288 C 2.1485 -1.6992 0.2375
> > > QMMM: 11 8289 C 4.2659 -3.1540 -0.0661
> > > QMMM: 12 8290 N 5.5728 -2.8904 0.4947
> > > QMMM: 13 8291 H 6.3540 -2.4813 0.0042
> > > QMMM: 14 8292 N 4.3212 -3.8931 -1.3111
> > > QMMM: 15 8293 H 4.3526 -3.4679 -2.2256
> > > QMMM: 16 8294 C 5.8271 -3.5267 1.6237
> > > QMMM: 17 8295 O 6.7660 -3.3274 2.3438
> > > QMMM: 18 8296 N 0.2067 -2.5201 1.0981
> > > QMMM: 19 8297 C -0.4168 -3.4512 1.9251
> > > QMMM: 20 8298 H -1.4679 -3.3216 2.1703
> > >
> > >
> > > Thanks and regards
> > > vinod
> > > _______________________________________________
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> >
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Received on Wed Oct 12 2011 - 10:00:02 PDT
