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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Received on Tue Oct 11 2011 - 09:30:04 PDT
