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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Oct 12 2011 - 06:00:03 PDT
